diff --git a/README.md b/README.md index 80d4486e..54c573ad 100644 --- a/README.md +++ b/README.md @@ -88,8 +88,7 @@ PATH and 'lib' must be accessible in the PYTHONPATH. ### 3. Install dependencies - Dependencies must be accessible in the PATH or added in - /libexec. + Dependencies must be accessible in the PATH or added in /libexec. python interpreter Version: 2.7 @@ -136,13 +135,13 @@ RDPClassifier Version: - - Name as: classifier.jar + Named as: classifier.jar Tools: affiliation_OTU Download: https://github.com/rdpstaff/RDPTools taskset Version: util-linux-ng 2.17.2 - Name as: taskset + Named as: taskset Tools: affiliation_OTU Install: sudo apt-get install util-linux OR @@ -166,6 +165,45 @@ Tools: tree Download: http://www.microbesonline.org/fasttree/#Install + RScript + Version : >= 3.3.0 + Named as : RScript + Tools : all FROGS_Phyloseq and FROGS_DESeq + Download : https://cran.r-project.org/ + + Rmarkdown R package + Version : depending on your R version + Tools : all FROGS_Phyloseq and FROGS_DESeq + Install in R session : # https://cran.r-project.org/web/packages/rmarkdown/index.html + install.packages("rmarkdown") + + Pandoc + Version : >= 1.12.3 + Named as : pandoc + Tools : all FROGS_Phyloseq and FROGS_DESeq + Download/Installation : # http://pandoc.org/installing.html#linux or simply soft-link pandoc binary from RStudio path (if you have Rstudio installed) + + Phyloseq R package + Version : depending on your R version + Tools : all FROGS_Phyloseq + Installation in R session : # https://joey711.github.io/phyloseq/install.html + source("https://bioconductor.org/biocLite.R") ; biocLite("phyloseq") + Test in R session : library(phyloseq) + + Plotly R package + Version : depending on your R version + Tools : FROGS_Phyloseq_composition and FROGS_Phyloseq_structure + Installation in R session : # https://plot.ly/r/getting-started/ + install.packages("plotly") + Test in R session : library(plotly) + + GridExtra R package + Version : depending on your R version + Tools : FROGS_Phyloseq_Beta_Diversity, FROGS_Phyloseq_Sample_Clustering, FROGS_Phyloseq_composition and FROGS_Phyloseq_structure + Installation in R session : # https://cran.r-project.org/web/packages/gridExtra/index.html + install.packages("gridExtra") + Test in R session : library(gridExtra) + ### 4. Check intallation To check your installation you can type: cd /test diff --git a/RELEASES_NOTES.md b/RELEASES_NOTES.md index 708d5a12..bd4b1f49 100644 --- a/RELEASES_NOTES.md +++ b/RELEASES_NOTES.md @@ -1,6 +1,13 @@ # v2.0.0 [DEV] ### Tools added : * Tree : perform phylogenetic tree reconstruction based on Pynast or Mafft and Fasttree + * FROGS Phyloseq Import Data : import data from 3 files: biomfile, samplefile, treefile into a phyloseq R object. + * FROGS Phyloseq Composition Visualization with bar plot and composition plot + * FROGS Phyloseq Alpha Diversity with richness plot + * FROGS Phyloseq Beta Diversity distance matrix + * FROGS Phyloseq Structure + * FROGS Phyloseq Clustering + * FROGS Phyloseq Manova ### Bugs fixes: * Preprocess : min overlap at least equal to 1 diff --git a/app/r_alpha_diversity.Rmd b/app/r_alpha_diversity.Rmd new file mode 120000 index 00000000..7f751f24 --- /dev/null +++ b/app/r_alpha_diversity.Rmd @@ -0,0 +1 @@ +../tools/phylo_alpha_diversity/r_alpha_diversity.Rmd \ No newline at end of file diff --git a/app/r_alpha_diversity.py b/app/r_alpha_diversity.py new file mode 120000 index 00000000..6cedfb3f --- /dev/null +++ b/app/r_alpha_diversity.py @@ -0,0 +1 @@ +../tools/phylo_alpha_diversity/r_alpha_diversity.py \ No newline at end of file diff --git a/app/r_alpha_diversity.xml b/app/r_alpha_diversity.xml new file mode 120000 index 00000000..ae960d09 --- /dev/null +++ b/app/r_alpha_diversity.xml @@ -0,0 +1 @@ +../tools/phylo_alpha_diversity/r_alpha_diversity.xml \ No newline at end of file diff --git a/app/r_beta_diversity.Rmd b/app/r_beta_diversity.Rmd new file mode 120000 index 00000000..6ea866a9 --- /dev/null +++ b/app/r_beta_diversity.Rmd @@ -0,0 +1 @@ +../tools/phylo_beta_diversity/r_beta_diversity.Rmd \ No newline at end of file diff --git a/app/r_beta_diversity.py b/app/r_beta_diversity.py new file mode 120000 index 00000000..461847bb --- /dev/null +++ b/app/r_beta_diversity.py @@ -0,0 +1 @@ +../tools/phylo_beta_diversity/r_beta_diversity.py \ No newline at end of file diff --git a/app/r_beta_diversity.xml b/app/r_beta_diversity.xml new file mode 120000 index 00000000..af3c97cf --- /dev/null +++ b/app/r_beta_diversity.xml @@ -0,0 +1 @@ +../tools/phylo_beta_diversity/r_beta_diversity.xml \ No newline at end of file diff --git a/app/r_clustering.Rmd b/app/r_clustering.Rmd new file mode 120000 index 00000000..57231b0a --- /dev/null +++ b/app/r_clustering.Rmd @@ -0,0 +1 @@ +../tools/phylo_clustering/r_clustering.Rmd \ No newline at end of file diff --git a/app/r_clustering.py b/app/r_clustering.py new file mode 120000 index 00000000..fe8bbe66 --- /dev/null +++ b/app/r_clustering.py @@ -0,0 +1 @@ +../tools/phylo_clustering/r_clustering.py \ No newline at end of file diff --git a/app/r_clustering.xml b/app/r_clustering.xml new file mode 120000 index 00000000..6d275c5e --- /dev/null +++ b/app/r_clustering.xml @@ -0,0 +1 @@ +../tools/phylo_clustering/r_clustering.xml \ No newline at end of file diff --git a/app/r_composition.Rmd b/app/r_composition.Rmd new file mode 120000 index 00000000..fd1dbb86 --- /dev/null +++ b/app/r_composition.Rmd @@ -0,0 +1 @@ +../tools/phylo_composition/r_composition.Rmd \ No newline at end of file diff --git a/app/r_composition.py b/app/r_composition.py new file mode 120000 index 00000000..ee1df9fb --- /dev/null +++ b/app/r_composition.py @@ -0,0 +1 @@ +../tools/phylo_composition/r_composition.py \ No newline at end of file diff --git a/app/r_composition.xml b/app/r_composition.xml new file mode 120000 index 00000000..9a7e3e0b --- /dev/null +++ b/app/r_composition.xml @@ -0,0 +1 @@ +../tools/phylo_composition/r_composition.xml \ No newline at end of file diff --git a/app/r_import_data.Rmd b/app/r_import_data.Rmd new file mode 120000 index 00000000..fe618fc6 --- /dev/null +++ b/app/r_import_data.Rmd @@ -0,0 +1 @@ +../tools/phylo_import/r_import_data.Rmd \ No newline at end of file diff --git a/app/r_import_data.py b/app/r_import_data.py new file mode 120000 index 00000000..2ea462cb --- /dev/null +++ b/app/r_import_data.py @@ -0,0 +1 @@ +../tools/phylo_import/r_import_data.py \ No newline at end of file diff --git a/app/r_import_data.xml b/app/r_import_data.xml new file mode 120000 index 00000000..922b91d5 --- /dev/null +++ b/app/r_import_data.xml @@ -0,0 +1 @@ +../tools/phylo_import/r_import_data.xml \ No newline at end of file diff --git a/app/r_manova.Rmd b/app/r_manova.Rmd new file mode 120000 index 00000000..fe7e3164 --- /dev/null +++ b/app/r_manova.Rmd @@ -0,0 +1 @@ +../tools/phylo_manova/r_manova.Rmd \ No newline at end of file diff --git a/app/r_manova.py b/app/r_manova.py new file mode 120000 index 00000000..f6379741 --- /dev/null +++ b/app/r_manova.py @@ -0,0 +1 @@ +../tools/phylo_manova/r_manova.py \ No newline at end of file diff --git a/app/r_manova.xml b/app/r_manova.xml new file mode 120000 index 00000000..e577074d --- /dev/null +++ b/app/r_manova.xml @@ -0,0 +1 @@ +../tools/phylo_manova/r_manova.xml \ No newline at end of file diff --git a/app/r_structure.Rmd b/app/r_structure.Rmd new file mode 120000 index 00000000..b2f70b5e --- /dev/null +++ b/app/r_structure.Rmd @@ -0,0 +1 @@ +../tools/phylo_structure/r_structure.Rmd \ No newline at end of file diff --git a/app/r_structure.py b/app/r_structure.py new file mode 120000 index 00000000..ba50d638 --- /dev/null +++ b/app/r_structure.py @@ -0,0 +1 @@ +../tools/phylo_structure/r_structure.py \ No newline at end of file diff --git a/app/r_structure.xml b/app/r_structure.xml new file mode 120000 index 00000000..a8c5cc97 --- /dev/null +++ b/app/r_structure.xml @@ -0,0 +1 @@ +../tools/phylo_structure/r_structure.xml \ No newline at end of file diff --git a/img/biomfile.png b/img/biomfile.png new file mode 100755 index 00000000..cfc7cb79 Binary files /dev/null and b/img/biomfile.png differ diff --git a/img/frogs_tree_view_phyloviz.png b/img/frogs_tree_view_phyloviz.png deleted file mode 100755 index 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b/img/phyloseq_samplefile.png differ diff --git a/tools/biom_to_tsv/biom_to_tsv.py b/tools/biom_to_tsv/biom_to_tsv.py index 6cc4e3a2..375ed891 100755 --- a/tools/biom_to_tsv/biom_to_tsv.py +++ b/tools/biom_to_tsv/biom_to_tsv.py @@ -61,6 +61,7 @@ def __init__( self, out_tsv, in_biom, in_fasta=None ): # Check the metadata biom = BiomIO.from_json( in_biom ) + obs = biom.rows[0] conversion_tags = "" if biom.has_observation_metadata( 'rdp_taxonomy' ) and biom.has_observation_metadata( 'rdp_bootstrap' ): conversion_tags += "'@rdp_tax_and_bootstrap' " @@ -76,6 +77,12 @@ def __init__( self, out_tsv, in_biom, in_fasta=None ): conversion_tags += "'seed_id' " if in_fasta is not None: conversion_tags += "'@seed_sequence' " + + frogs_metadata = ["rdp_taxonomy", "rdp_bootstrap","blast_taxonomy","blast_affiliations","seed_id"] + for metadata in biom.get_observation_metadata(obs["id"]): + if metadata not in frogs_metadata : + conversion_tags += "'"+metadata+"' " + conversion_tags += "'@observation_name' '@observation_sum' '@sample_count'" # Set command diff --git a/tools/phylo_alpha_diversity/data/data.Rdata b/tools/phylo_alpha_diversity/data/data.Rdata new file mode 100755 index 00000000..aca7595e Binary files /dev/null and b/tools/phylo_alpha_diversity/data/data.Rdata differ diff --git a/tools/phylo_alpha_diversity/r_alpha_diversity.Rmd b/tools/phylo_alpha_diversity/r_alpha_diversity.Rmd new file mode 100755 index 00000000..a65dbded --- /dev/null +++ b/tools/phylo_alpha_diversity/r_alpha_diversity.Rmd @@ -0,0 +1,572 @@ +--- +output: html_document +params: + data: + value: x + measures: + value: x + varExp: + value: x + fileAlpha: + value: x +--- + + + + + + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` +

FROGS Phyloseq: Alpha Diversity Visualization

+ + Phyloseq `r packageVersion("phyloseq")` + +```{r include=FALSE, cache=FALSE} +library(phyloseq) +library(ggplot2) +load(params$data) +measures <- as.list(strsplit(params$measures, ",")[[1]]) +``` + +```{r, echo=FALSE} +## Numeric values of alpha diversity indices +alpha.diversity <- estimate_richness(data, measures = measures) + +## export diversity to text file +write.table(alpha.diversity, params$fileAlpha, sep="\t", quote = FALSE, col.names = NA) +``` + +#{.tabset .tabset-fade .tabset-pills} +##Richness plot +```{r, fig.width=10, fig.height=8, echo=FALSE, comment=NA, warning=FALSE} +p <- plot_richness(data, x = params$varExp, color = params$varExp, measures = measures) + ggtitle(paste("Alpha diversity distribution in function of", params$varExp))+ theme(plot.title = element_text(hjust = 0.5)) +plot(p) +``` +
+ + +##Richness plot with boxplot +```{r, fig.width=10, fig.height=8, echo=FALSE, comment=NA, warning=FALSE} +p <- p + geom_boxplot(alpha = 0.2) + + geom_point()+ theme_grey() + + theme(axis.text.x = element_text(angle=90, hjust=0.5)) + + theme(plot.title = element_text(hjust = 0.5)) +plot(p) +``` +
+ + +##Alpha Diversity Indice Anova Analysis +```{r, echo=FALSE, comment=NA} +anova_data <- cbind(sample_data(data), alpha.diversity) +anova_data$Depth <- sample_sums(data) + +variables=c() +for (var in sample_variables(data) ) { + l = length(levels(as.factor(get_variable(data,var)))) + if(l > 1 && l < nsamples(data)){ + variables <- cbind(variables,var) + } +} +variables <- paste(sep=" + ", "Depth", paste(collapse =" + ", variables )) +## Perform ANOVA on observed richness, which effects are significant +for (m in measures){ + f <- paste(m," ~ ", variables) + cat(sep = "", "###############################################################\n#Perform ANOVA on ",m,", which effects are significant\nanova.",m," <-aov( ",f,", anova_data)\nsummary(anova.",m,")\n") + anova_res <- aov( as.formula(f), anova_data) + res <- summary(anova_res) + print(res) + cat("\n\n") +} +``` + +##Rarefaction curves +```{r include=FALSE, cache=FALSE} +##code of Mahendra Mariadassou +library(parallel) +library(vegan) +## Rarefaction curve, ggplot style +ggrare <- function(physeq, step = 10, label = NULL, color = NULL, plot = TRUE, parallel = FALSE, se = TRUE) { + ## Args: + ## - physeq: phyloseq class object, from which abundance data are extracted + ## - step: Step size for sample size in rarefaction curves + ## - label: Default `NULL`. Character string. The name of the variable + ## to map to text labels on the plot. Similar to color option + ## but for plotting text. + ## - color: (Optional). Default ‘NULL’. Character string. The name of the + ## variable to map to colors in the plot. This can be a sample + ## variable (among the set returned by + ## ‘sample_variables(physeq)’ ) or taxonomic rank (among the set + ## returned by ‘rank_names(physeq)’). + ## + ## Finally, The color scheme is chosen automatically by + ## ‘link{ggplot}’, but it can be modified afterward with an + ## additional layer using ‘scale_color_manual’. + ## - color: Default `NULL`. Character string. The name of the variable + ## to map to text labels on the plot. Similar to color option + ## but for plotting text. + ## - plot: Logical, should the graphic be plotted. + ## - parallel: should rarefaction be parallelized (using parallel framework) + ## - se: Default TRUE. Logical. Should standard errors be computed. + ## require vegan + x <- as(otu_table(physeq), "matrix") + if (taxa_are_rows(physeq)) { x <- t(x) } + + ## This script is adapted from vegan `rarecurve` function + tot <- rowSums(x) + S <- rowSums(x > 0) + nr <- nrow(x) + + rarefun <- function(i) { + cat(paste("rarefying sample", rownames(x)[i]), sep = "\n") + n <- seq(1, tot[i], by = step) + if (n[length(n)] != tot[i]) { + n <- c(n, tot[i]) + } + y <- rarefy(x[i, ,drop = FALSE], n, se = se) + if (nrow(y) != 1) { + rownames(y) <- c(".S", ".se") + return(data.frame(t(y), Size = n, Sample = rownames(x)[i])) + } else { + return(data.frame(.S = y[1, ], Size = n, Sample = rownames(x)[i])) + } + } + if (parallel) { + out <- mclapply(seq_len(nr), rarefun, mc.preschedule = FALSE) + } else { + out <- lapply(seq_len(nr), rarefun) + } + df <- do.call(rbind, out) + + ## Get sample data + if (!is.null(sample_data(physeq, FALSE))) { + sdf <- as(sample_data(physeq), "data.frame") + sdf$Sample <- rownames(sdf) + data <- merge(df, sdf, by = "Sample") + labels <- data.frame(x = tot, y = S, Sample = rownames(x)) + labels <- merge(labels, sdf, by = "Sample") + } + + ## Add, any custom-supplied plot-mapped variables + if( length(color) > 1 ){ + data$color <- color + names(data)[names(data)=="color"] <- deparse(substitute(color)) + color <- deparse(substitute(color)) + } + if( length(label) > 1 ){ + labels$label <- label + names(labels)[names(labels)=="label"] <- deparse(substitute(label)) + label <- deparse(substitute(label)) + } + + p <- ggplot(data = data, aes_string(x = "Size", y = ".S", group = "Sample", color = color)) + p <- p + labs(x = "Sample Size", y = "Species Richness") + if (!is.null(label)) { + p <- p + geom_text(data = labels, aes_string(x = "x", y = "y", label = label, color = color), + size = 4, hjust = 0) + } + p <- p + geom_line() + if (se) { ## add standard error if available + p <- p + geom_ribbon(aes_string(ymin = ".S - .se", ymax = ".S + .se", color = NULL, fill = color), alpha = 0.2) + } + if (plot) { + plot(p) + } + invisible(p) +} + +p <- ggrare(data, step = 500, color = params$varExp, plot = FALSE) +rare.level <- sample_sums(data)[[1]] +``` + +```{r, fig.width=10, fig.height=8, echo=FALSE, comment=NA, warning=FALSE} +po <- paste('p + facet_wrap(~',params$varExp,') + geom_vline(xintercept = rare.level, color = "gray60")') +eval(parse(text = po)) +plot(p) +``` +
+ + +##R code +

Loading packages & data

+```{r, comment=NA, cache=FALSE, echo=FALSE} +measures <- gsub(",", '","', paste('c("', params$measures, '")', sep="")) +cat("#if in new session \n#data <- path to Rdata file \n#load(data)\n#library(phyloseq)\n#library(ggplot2)") +cat(paste("varExp <- ", params$varExp)) +cat(paste("measures <- ", measures)) +cat("fileAlpha <- \"alpha_diversity.tsv\"") +``` + +

Save alpha distance table

+```{r, comment=NA, cache=FALSE, echo=FALSE} +cat(paste("fileAlpha <- #path to output Alpha diversity file\nalpha.diversity <- estimate_richness(data, measures = measures )"), "\nwrite.table(alpha.diversity, fileAlpha, sep='\\t', quote = FALSE, col.names = NA)") +``` + +

Richness plot

+```{r, comment=NA, cache=FALSE, echo=FALSE} +cat(paste(sep="","p <- plot_richness(data, x = ", '"', params$varExp,'"', ", color = ", '"', params$varExp, '"', ", measures = measures )", '+ ggtitle("Alpha diversity distribution in function of ', params$varExp, '")'),'+ theme(plot.title = element_text(hjust = 0.5))', '\nplot(p)') +``` + +

With box plot

+```{r, comment=NA, cache=FALSE, echo=FALSE} +cat('p <- p + geom_boxplot(alpha = 0.2) + theme_bw() + geom_point() + theme(axis.text.x = element_blank(), plot.title = element_text(hjust = 0.5))\nplot(p)') +``` + +

Anova analysis

+```{r, comment=NA, eval=FALSE} +anova_data <- cbind(sample_data(data), alpha.diversity) +anova_data$Depth <- sample_sums(data) +variables=c() +for (var in sample_variables(data) ) { + l = length(levels(as.factor(get_variable(data,var)))) + if(l > 1 && l < nsamples(data)){ + variables <- cbind(variables,var) + } +} +variables <- paste(sep=" + ", "Depth", paste(collapse =" + ", variables )) +## Perform ANOVA on observed richness, which effects are significant +for (m in measures){ + f <- paste(m," ~ ", variables) + cat(sep = "", "###############################################################\n + #Perform ANOVA on ",m,", which effects are significant\n + anova.",m," <-aov( ",f,", anova_data)\n + summary(anova.",m,")\n") + anova_res <- aov( as.formula(f), anova_data) + res <- summary(anova_res) + print(res) + cat("\n\n") +} +``` + +

The rarefaction curve

+```{r, eval=FALSE} +##code of Mahendra Mariadassou for the rarefaction curve +library(parallel) +library(vegan) + +## Rarefaction curve, ggplot style +ggrare <- function(physeq, step = 10, label = NULL, color = NULL, plot = TRUE, parallel = FALSE, se = TRUE) { + ## Args: + ## - physeq: phyloseq class object, from which abundance data are extracted + ## - step: Step size for sample size in rarefaction curves + ## - label: Default `NULL`. Character string. The name of the variable + ## to map to text labels on the plot. Similar to color option + ## but for plotting text. + ## - color: (Optional). Default ‘NULL’. Character string. The name of the + ## variable to map to colors in the plot. This can be a sample + ## variable (among the set returned by + ## ‘sample_variables(physeq)’ ) or taxonomic rank (among the set + ## returned by ‘rank_names(physeq)’). + ## + ## Finally, The color scheme is chosen automatically by + ## ‘link{ggplot}’, but it can be modified afterward with an + ## additional layer using ‘scale_color_manual’. + ## - color: Default `NULL`. Character string. The name of the variable + ## to map to text labels on the plot. Similar to color option + ## but for plotting text. + ## - plot: Logical, should the graphic be plotted. + ## - parallel: should rarefaction be parallelized (using parallel framework) + ## - se: Default TRUE. Logical. Should standard errors be computed. + ## require vegan + x <- as(otu_table(physeq), "matrix") + if (taxa_are_rows(physeq)) { x <- t(x) } + + ## This script is adapted from vegan `rarecurve` function + tot <- rowSums(x) + S <- rowSums(x > 0) + nr <- nrow(x) + + rarefun <- function(i) { + cat(paste("rarefying sample", rownames(x)[i]), sep = "\n") + n <- seq(1, tot[i], by = step) + if (n[length(n)] != tot[i]) { + n <- c(n, tot[i]) + } + y <- rarefy(x[i, ,drop = FALSE], n, se = se) + if (nrow(y) != 1) { + rownames(y) <- c(".S", ".se") + return(data.frame(t(y), Size = n, Sample = rownames(x)[i])) + } else { + return(data.frame(.S = y[1, ], Size = n, Sample = rownames(x)[i])) + } + } + if (parallel) { + out <- mclapply(seq_len(nr), rarefun, mc.preschedule = FALSE) + } else { + out <- lapply(seq_len(nr), rarefun) + } + df <- do.call(rbind, out) + + ## Get sample data + if (!is.null(sample_data(physeq, FALSE))) { + sdf <- as(sample_data(physeq), "data.frame") + sdf$Sample <- rownames(sdf) + data <- merge(df, sdf, by = "Sample") + labels <- data.frame(x = tot, y = S, Sample = rownames(x)) + labels <- merge(labels, sdf, by = "Sample") + } + + ## Add, any custom-supplied plot-mapped variables + if( length(color) > 1 ){ + data$color <- color + names(data)[names(data)=="color"] <- deparse(substitute(color)) + color <- deparse(substitute(color)) + } + if( length(label) > 1 ){ + labels$label <- label + names(labels)[names(labels)=="label"] <- deparse(substitute(label)) + label <- deparse(substitute(label)) + } + + p <- ggplot(data = data, aes_string(x = "Size", y = ".S", group = "Sample", color = color)) + p <- p + labs(x = "Sample Size", y = "Species Richness") + if (!is.null(label)) { + p <- p + geom_text(data = labels, aes_string(x = "x", y = "y", label = label, color = color), + size = 4, hjust = 0) + } + p <- p + geom_line() + if (se) { ## add standard error if available + p <- p + geom_ribbon(aes_string(ymin = ".S - .se", ymax = ".S + .se", color = NULL, fill = color), alpha = 0.2) + } + if (plot) { + plot(p) + } + invisible(p) +} + +p <- ggrare(data, step = 500, color = varExp, plot = FALSE) +rare.level <- sample_sums(data)[[1]] +capcap <- paste('p <- p + facet_wrap(~', varExp, ') + geom_vline(xintercept = rare.level, color = "gray60")') +eval(parse(text = capcap)) +plot(p) +``` + + + + + + + diff --git a/tools/phylo_alpha_diversity/r_alpha_diversity.py b/tools/phylo_alpha_diversity/r_alpha_diversity.py new file mode 100755 index 00000000..387dac57 --- /dev/null +++ b/tools/phylo_alpha_diversity/r_alpha_diversity.py @@ -0,0 +1,105 @@ +#!/usr/bin/env python2.7 +# +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +# +__author__ = 'Ta Thi Ngan & Maria Bernard INRA - SIGENAE' +__copyright__ = 'Copyright (C) 2017 INRA' +__license__ = 'GNU General Public License' +__version__ = '1.0.0' +__email__ = 'frogs@toulouse.inra.fr' +__status__ = 'prod' + +import os +import sys +import argparse + +CURRENT_DIR = os.path.dirname(os.path.abspath(__file__)) +# PATH +BIN_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "libexec")) +os.environ['PATH'] = BIN_DIR + os.pathsep + os.environ['PATH'] +# PYTHONPATH +LIB_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "lib")) +sys.path.append(LIB_DIR) +if os.getenv('PYTHONPATH') is None: os.environ['PYTHONPATH'] = LIB_DIR +else: os.environ['PYTHONPATH'] = os.environ['PYTHONPATH'] + os.pathsep + LIB_DIR + +from frogsUtils import * +################################################################################################################################################## +# +# COMMAND LINES +# +################################################################################################################################################## + +class Rscript(Cmd): + """ + @summary: Launch Rmarkdown script to present the alpha diversity of data with phyloseq. + @see: http://rmarkdown.rstudio.com/ + https://joey711.github.io/phyloseq/ + @return: html file containing the plots + alpha divesity table + """ + def __init__(self, data, html, varExp, measures, alphaD): + """ + @param data: [str] path to phyloseq object in RData file, the result of FROGS Phyloseq Import Data. + @param html: [str] Path to store resulting html file. + @param varExp: [str] Experiment variable used to aggregate sample diversities. + @param measures: [str] The indexes of alpha diversity, in list (Observed, Chao1, Shannon, Simpson, InvSimpson, ACE, Fisher). + @param alphaD: [str] Path to store resulting data file containing alpha diversity table. + """ + rmd = os.path.join(CURRENT_DIR, "r_alpha_diversity.Rmd") + Cmd.__init__( self, + 'Rscript', + 'Run 1 code Rmarkdown', + '-e "rmarkdown::render('+"'"+rmd+"',output_file='"+html+"', params=list(data='"+data+"', measures='"+measures+"', varExp='"+varExp+"',fileAlpha='"+alphaD+"'), intermediates_dir='"+os.path.dirname(html)+"')"+'" 2> /dev/null', + "-e '(sessionInfo()[[1]][13])[[1]][1]; paste(\"Rmarkdown version: \",packageVersion(\"rmarkdown\")) ; library(phyloseq); paste(\"Phyloseq version: \",packageVersion(\"phyloseq\"))'") + def get_version(self): + """ + @summary: Returns the program version number. + @return: [str] Version number if this is possible, otherwise this method return 'unknown'. + """ + return Cmd.get_version(self, 'stdout') + +################################################################################################################################################## +# +# MAIN +# +################################################################################################################################################## + +if __name__ == "__main__": + + # Manage parameters + parser = argparse.ArgumentParser( description='To compute and present the data alpha diversity with plot_richness of Phyloseq.' ) + parser.add_argument('-v', '--varExp', type=str, required=True, default=None, help='The experiment variable used to aggregate sample diversities.' ) + parser.add_argument('-m', '--measures', type=str, required=True, nargs="*", default=['Observed','Chao1','Shannon','InvSimpson'], help='The indexes of alpha diversity, in list "Observed,Chao1,Shannon,InvSimpson,Simpson,ACE,Fisher". Each index is separated by one comma. [Default: %(default)s]') + + # Inputs + group_input = parser.add_argument_group( 'Inputs' ) + group_input.add_argument('-d','--data', required=True, default=None, help="The path of RData file containing a phyloseq object-the result of FROGS Phyloseq Import Data" ) + + # output + group_output = parser.add_argument_group( 'Outputs' ) + group_output.add_argument('-o','--html', default='alpha_diversity.html', help="The path to store resulting html file. [Default: %(default)s]" ) + group_output.add_argument('-a','--alphaD', default='alpha_diversity.tsv', help="The path to store resulting data file containing alpha diversity table. [Default: %(default)s]" ) + group_output.add_argument( '-l', '--log_file', default=sys.stdout, help="This output file will contain several information on executed commands.") + args = parser.parse_args() + prevent_shell_injections(args) + # Process + Logger.static_write(args.log_file, "## Application\nSoftware :" + sys.argv[0] + " (version : " + str(__version__) + ")\nCommand : " + " ".join(sys.argv) + "\n\n") + data=os.path.abspath(args.data) + html=os.path.abspath(args.html) + alphaD=os.path.abspath(args.alphaD) + measures=",".join(args.measures) + Rscript(data, html, args.varExp, measures, alphaD).submit( args.log_file ) diff --git a/tools/phylo_alpha_diversity/r_alpha_diversity.xml b/tools/phylo_alpha_diversity/r_alpha_diversity.xml new file mode 100755 index 00000000..4a5401d8 --- /dev/null +++ b/tools/phylo_alpha_diversity/r_alpha_diversity.xml @@ -0,0 +1,110 @@ + + + + with richness plot + r_alpha_diversity.py + --data $data + --varExp $varExp + --measures $measures + --alphaD $alphaD + --html $html + + + + + + + + + + + + + + + + + + + + + + + + + + +.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and customized R function, this tool constructs richness plots to visualise sample alpha diversity. + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**Data file** (format RData): +One phyloseq object containing OTU abundance table, their taxonomies (and optionnaly a phylogenetics tree, and the sample experiment metadata. +This file is the result of "FROGS Phyloseq Import Data tool". + +.. class:: h3 + +Output + +**Html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): the review of richness plots and rarefaction curves. + +.. image:: ${static_path}/images/tools/frogs/phyloseq_plot_richness.png + :height: 400 + :width: 525 + +.. image:: ${static_path}/images/tools/frogs/phyloseq_plot_richness_box.png + :height: 400 + :width: 499 + +.. image:: ${static_path}/images/tools/frogs/phyloseq_rarefaction_curves.png + :height: 400 + :width: 498 + +**Alpha diversity table** (alpha_diversity.tsv): +The data file containing table of alpha diversity indices. + +.. image:: ${static_path}/images/tools/frogs/phyloseq_alpha_diversity_table.png + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@toulouse.inra.fr + +Repository: https://github.com/geraldinepascal/FROGS + +Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf + +Depending on the help provided you can cite us in acknowledgements, references or both. + + + diff --git a/tools/phylo_alpha_diversity/test.sh b/tools/phylo_alpha_diversity/test.sh new file mode 100755 index 00000000..a23746b1 --- /dev/null +++ b/tools/phylo_alpha_diversity/test.sh @@ -0,0 +1,14 @@ +#!/bin/sh +export PATH=../../libexec:$PATH +export PYTHONPATH=../../lib:$PYTHONPATH + +if [ -d test ] +then + rm -r test/* +else + mkdir test +fi + +python r_alpha_diversity.py -d data/data.Rdata \ + -v EnvType -m Observed Chao1 Shannon \ + -l test/phylo_alpha.log -o test/phylo_alpha.html -a test/phylo_alpha.tsv diff --git a/tools/phylo_beta_diversity/data/data.Rdata b/tools/phylo_beta_diversity/data/data.Rdata new file mode 100755 index 00000000..aca7595e Binary files /dev/null and b/tools/phylo_beta_diversity/data/data.Rdata differ diff --git a/tools/phylo_beta_diversity/r_beta_diversity.Rmd b/tools/phylo_beta_diversity/r_beta_diversity.Rmd new file mode 100755 index 00000000..f04bba3b --- /dev/null +++ b/tools/phylo_beta_diversity/r_beta_diversity.Rmd @@ -0,0 +1,233 @@ +--- +output: html_document +params: + data: + value: x + varExp: + value: x + methods: + value: x +--- + + + + + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` +

FROGS Phyloseq: Beta Diversity Visualization

+ + Phyloseq `r packageVersion("phyloseq")` + +```{r include=FALSE, cache=FALSE} +library(phyloseq) +library(ggplot2) +library(gridExtra) +library(reshape2) +load(params$data) +``` + +```{r include=FALSE, cache=FALSE, comment=NA} +## Generic method for distance +methods <- as.list(strsplit(params$methods, ",")[[1]]) + +## code to visualize distances of Mahendra Mariadassou +sampleOrder <- levels(reorder(sample_names(data), as.numeric(get_variable(data, params$varExp)))) + +plot_dist_as_heatmap <- function(dist, order = sampleOrder, title = NULL) { + data <- melt(as(dist, "matrix")) + colnames(data) <- c("x", "y", "distance") + if (!is.null(order)) { + data$x <- factor(data$x, levels = order) + data$y <- factor(data$y, levels = order) + } + p <- ggplot(data, aes(x = x, y = y, fill = distance)) + geom_tile() + p <- p + theme(axis.title.x = element_blank(), + axis.title.y = element_blank(), + axis.text.x = element_blank(), + axis.text.y = element_blank() + ) + p <- p + scale_fill_continuous(limits = c(0, 1)) + if (!is.null(title)) { + p <- p + ggtitle(title) + } + return(p) +} +``` + +#{.tabset .tabset-fade .tabset-pills} + +##Dist as heatmap plot +```{r, fig.width=8, fig.height=6, echo=FALSE, warning=FALSE} + +for (method in methods){ + if (method=="unifrac"){ + dist.uf <- distance(data, method = "unifrac") ## Unifrac + uf <- as.matrix(dist.uf) + write.table(uf, "Unifrac.tsv", sep="\t", quote=FALSE, col.names=NA) + p1 <- plot_dist_as_heatmap(dist.uf, title = "Unifrac")+ theme(plot.title = element_text(hjust = 0.5)) + plot(p1) + }else if (method=="wunifrac"){ + dist.wuf <- distance(data, method = "wunifrac") ## Weighted Unifrac + wuf <- as.matrix(dist.wuf) + write.table(wuf, "wUnifrac.tsv",sep="\t", quote=FALSE, col.names=NA) + p2 <- plot_dist_as_heatmap(dist.wuf, title = "wUnifrac")+ theme(plot.title = element_text(hjust = 0.5)) + plot(p2) + }else if (method=="bray"){ + dist.bc <- distance(data, method = "bray") ## Bray-Curtis + bc <- as.matrix(dist.bc) + write.table(bc, "Bray_Curtis.tsv",sep="\t", quote=FALSE, col.names=NA) + p3 <- plot_dist_as_heatmap(dist.bc, title = "Bray-Curtis")+ theme(plot.title = element_text(hjust = 0.5)) + plot(p3) + }else if (method=="cc"){ + dist.jac <- distance(data, method = "cc") ## Jaccard + jac <- as.matrix(dist.jac) + write.table(jac, "Jaccard.tsv",sep="\t", quote=FALSE, col.names=NA) + p4 <- plot_dist_as_heatmap(dist.jac, title = "Jaccard")+ theme(plot.title = element_text(hjust = 0.5)) + plot(p4) + }else { + dist.a <- distance(data, method = method) + a <- as.matrix(dist.a) + write.table(a, paste(sep="", method, ".tsv"), sep="\t", quote=FALSE, col.names=NA) + pa <- plot_dist_as_heatmap(dist.a, title = method)+ theme(plot.title = element_text(hjust = 0.5)) + plot(pa) + } +} +``` + +##R code +

Loading packages & data

+```{r, eval=FALSE} +library(phyloseq) +library(ggplot2) +library(gridExtra) +library(reshape2) +#if in new session +#data <- path to Rdata file +#load(data) +varExp <- #Experiment variable to split plot +method <- #Beta diversity method name #To show all available distances: distanceMethodList +fileBeta <- "beta_diversity.tsv" # output file path +``` + +

Dist as heatmap plot

+```{r, eval=FALSE} +## code to visualize distances of Mahendra Mariadassou +sampleOrder <- levels(reorder(sample_names(data), as.numeric(get_variable(data, varExp)))) + +plot_dist_as_heatmap <- function(dist, order = sampleOrder, title = NULL) { + data <- melt(as(dist, "matrix")) + colnames(data) <- c("x", "y", "distance") + if (!is.null(order)) { + data$x <- factor(data$x, levels = order) + data$y <- factor(data$y, levels = order) + } + p <- ggplot(data, aes(x = x, y = y, fill = distance)) + geom_tile() + p <- p + theme(axis.title.x = element_blank(), + axis.title.y = element_blank(), + axis.text.x = element_blank(), + axis.text.y = element_blank() + ) + p <- p + scale_fill_continuous(limits = c(0, 1)) + if (!is.null(title)) { + p <- p + ggtitle(title) + } + return(p) +} + +dist.a <- distance(data, method = method) + +pa <- plot_dist_as_heatmap(dist.a, title = method)+ theme(plot.title = element_text(hjust = 0.5)) +plot(pa) +``` + +

Save distance matrix

+```{r, eval=FALSE} +a <- as.matrix(dist.a) +write.table(a, fileBeta, sep="\t", quote=FALSE, col.names=NA) +``` + + + + + diff --git a/tools/phylo_beta_diversity/r_beta_diversity.py b/tools/phylo_beta_diversity/r_beta_diversity.py new file mode 100755 index 00000000..4b45bb91 --- /dev/null +++ b/tools/phylo_beta_diversity/r_beta_diversity.py @@ -0,0 +1,117 @@ +#!/usr/bin/env python2.7 +# +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +# +__author__ = 'Ta Thi Ngan & Maria Bernard INRA - SIGENAE' +__copyright__ = 'Copyright (C) 2017 INRA' +__license__ = 'GNU General Public License' +__version__ = '1.0.0' +__email__ = 'frogs@toulouse.inra.fr' +__status__ = 'prod' + +import os +import sys +import argparse + +CURRENT_DIR = os.path.dirname(os.path.abspath(__file__)) +# PATH +BIN_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "libexec")) +os.environ['PATH'] = BIN_DIR + os.pathsep + os.environ['PATH'] +# PYTHONPATH +LIB_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "lib")) +sys.path.append(LIB_DIR) +if os.getenv('PYTHONPATH') is None: os.environ['PYTHONPATH'] = LIB_DIR +else: os.environ['PYTHONPATH'] = os.environ['PYTHONPATH'] + os.pathsep + LIB_DIR + +from frogsUtils import * +################################################################################################################################################## +# +# COMMAND LINES +# +################################################################################################################################################## + +class Rscript(Cmd): + """ + @summary: Launch Rmarkdown script to present the data beta diversity with phyloseq. + @see: http://rmarkdown.rstudio.com/ + https://joey711.github.io/phyloseq/ + @return: html file containing the plots + beta divesity distance matrix tsv file(s) + """ + def __init__(self, html, data, varExp, methods, outdir): + """ + @param html: [str] path to store resulting html file. + @param data: [str] path to phyloseq object in RData file, the result of FROGS Phyloseq Import Data. + @param varExp: [str] Experiment variable to split plot. + @param methods: [str] one or more of beta diversity method. + @param outdir: [str] The path to store resulting beta diversity distance matrix. + """ + rmd = os.path.join(CURRENT_DIR, "r_beta_diversity.Rmd") + Cmd.__init__( self, + 'Rscript', + 'Run 1 code Rmarkdown', + '-e "rmarkdown::render('+"'"+rmd+"',knit_root_dir='"+outdir+ "',output_file='"+html+"', params=list(data='"+data+"', varExp='"+varExp+ "', methods='"+methods+ "'), intermediates_dir='"+os.path.dirname(html)+"')"+'" 2> /dev/null', + "-e '(sessionInfo()[[1]][13])[[1]][1]; paste(\"Rmarkdown version: \",packageVersion(\"rmarkdown\")) ; library(phyloseq); paste(\"Phyloseq version: \",packageVersion(\"phyloseq\"))'") + def get_version(self): + """ + @summary: Returns the program version number. + @return: [str] Version number if this is possible, otherwise this method return 'unknown'. + """ + return Cmd.get_version(self, 'stdout') + +################################################################################################################################################## +# +# MAIN +# +################################################################################################################################################## + +if __name__ == "__main__": + + # Manage parameters + parser = argparse.ArgumentParser( description='To present the data beta diversity with phyloseq.') + parser.add_argument('--output_dir', required=True, action="store", type=str, help="Path to output matrix file") + parser.add_argument('-v', '--varExp', type=str, required=True, default=None, help='The experiment variable you want to analyse.') + parser.add_argument('-m', '--methods', required=True, type=str, default='bray,cc,unifrac,wunifrac', help='The methods of beta diversity in Phyloseq distance list. Each method is separated by one comma. [Default: %(default)s].') + # Inputs + group_input = parser.add_argument_group( 'Inputs' ) + group_input.add_argument('-d','--data', required=True, default=None, help="The path of RData file containing a phyloseq object-the result of FROGS Phyloseq Import Data" ) + # output + group_output = parser.add_argument_group( 'Outputs' ) + group_output.add_argument('-o','--html', default='beta_diversity.html', help="Path to store resulting html file. [Default: %(default)s]" ) + group_output.add_argument( '-l', '--log_file', default=sys.stdout, help='This output file will contain several information on executed commands.') + args = parser.parse_args() + prevent_shell_injections(args) + + Logger.static_write(args.log_file, "## Application\nSoftware :" + sys.argv[0] + " (version : " + str(__version__) + ")\nCommand : " + " ".join(sys.argv) + "\n\n") + # check parameter + if args.methods=="None": + raise Exception("You must choose at least one method name.") + list_distance=["unifrac","wunifrac","bray","cc","dpcoa","jsd","manhattan","euclidean","canberra","kulczynski","jaccard","gower","altGower","morisita","horn","mountford","raup","binomial","chao","cao","w","-1","c","wb","r","I","e","t","me","j","sor","m","-2","co","g","-3","l","19","hk","rlb","sim","gl","z","maximum","binary","minkowski","ANY"] + + methods=args.methods.split(",") if not args.methods[-1] == "," else args.methods[:-1].split(",") + for method in methods: + if method not in list_distance: + raise Exception( 'Your method "'+str(method)+'", name is not correct !!! Please make sure that it is in the list:'+str(list_distance)) + + outdir = args.output_dir + if not os.path.exists(args.output_dir): + os.makedirs(args.output_dir) + outdir=os.path.abspath(outdir) + + # Process + data=os.path.abspath(args.data) + html=os.path.abspath(args.html) + Rscript(html, data, args.varExp, args.methods, outdir).submit( args.log_file ) diff --git a/tools/phylo_beta_diversity/r_beta_diversity.xml b/tools/phylo_beta_diversity/r_beta_diversity.xml new file mode 100755 index 00000000..70a34f7c --- /dev/null +++ b/tools/phylo_beta_diversity/r_beta_diversity.xml @@ -0,0 +1,110 @@ + + + + distance matrix + r_beta_diversity.py + --data $data + --varExp $varExp + --methods $methods,$other_method + --output_dir BetaMatrix + --html $html + + + + + + + + + + + + + + + + + + + + + + + + + +.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and customized R function, this tool compute beta distance matrix and display them in a heatmap + + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**data file** (format RData): +One phyloseq object containing OTU abundance table, their taxonomies and optionnaly a phylogenetic tree, and the sample experiment metadata. +This file is the result of "FROGS Phyloseq Import Data tool". + +**distance methods** : +The list of Phyloseq distanceMethodList is available here `distanceMethodList <https://www.bioconductor.org/packages/devel/bioc/manuals/phyloseq/man/phyloseq.pdf>`_ . +You have to copy the exact name as in this list in the parameter window "Other Method". +To use several methods, separate them by a space. + +.. class:: h3 + +Output + +**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): + +The review of beta diversity with heatmap plots: + +.. image:: ${static_path}/images/tools/frogs/phyloseq_beta_diversity.png + :height: 609 + :width: 800 + + +**beta diversity matrix** (format tabular): +The distance matrix of beta diversity. + + .. image:: ${static_path}/images/tools/frogs/phyloseq_beta_diversity_matrix.png + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@toulouse.inra.fr + +Repository: https://github.com/geraldinepascal/FROGS + +Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf + +Depending on the help provided you can cite us in acknowledgements, references or both. + + + diff --git a/tools/phylo_beta_diversity/test.sh b/tools/phylo_beta_diversity/test.sh new file mode 100755 index 00000000..3183d939 --- /dev/null +++ b/tools/phylo_beta_diversity/test.sh @@ -0,0 +1,18 @@ +#!/bin/sh +export PATH=../../libexec:$PATH +export PYTHONPATH=../../lib:$PYTHONPATH + +if [ -d test ] +then + rm -r test/* +else + mkdir test +fi + +python r_beta_diversity.py \ + --data data/data.Rdata \ + --varExp EnvType \ + --methods bray,unifrac,wunifrac,euclidean \ + --output_dir test \ + --html test/phylo_beta.html \ + --log_file test/phylo_beta.log diff --git a/tools/phylo_clustering/data/Unifrac.tsv b/tools/phylo_clustering/data/Unifrac.tsv new file mode 100755 index 00000000..ae7b4cb6 --- /dev/null +++ b/tools/phylo_clustering/data/Unifrac.tsv @@ -0,0 +1,65 @@ + DLT0.LOT08 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0.6500222935817 0.594526823867159 0.67515670410921 0.683096887784488 0.682711470208066 0.740384225726536 0.693949185684871 0.726661776225368 0.699855416029865 0.75680215530665 0.744725958835001 0.743937334398847 0.754062824994675 0.722966867698204 0.735637480902113 0.744714842477375 0.717597095987244 0.753160951420512 0.75234830854329 0.749813205981954 0.717495137115782 0.714231303951868 0.730151738606556 0.728768750286118 0.747856035417349 0.731521764361644 0.685895955777848 0.687755254485791 0.678835118079268 0.671732353452938 0.705247863394395 0.744590372287353 0.745826230004089 0.697402351555434 0.646987010604685 0.629434814020957 0.660966397226216 0.65320386908558 0.65363645674624 0.654488488337092 0.614518230668112 0.635655286777263 0.629849028501794 0.606756953431382 0.617126044949311 0.608508325835615 0.5703318787322 0.603744118941208 0.610825437383759 0.586250090947481 0.460366992888907 0.478627417163533 0.405724413028045 0.425623082702277 0.407702954758623 0.366536918145145 0.278078263394802 0 diff --git a/tools/phylo_clustering/data/data.Rdata b/tools/phylo_clustering/data/data.Rdata new file mode 100755 index 00000000..aca7595e Binary files /dev/null and b/tools/phylo_clustering/data/data.Rdata differ diff --git a/tools/phylo_clustering/r_clustering.Rmd b/tools/phylo_clustering/r_clustering.Rmd new file mode 100755 index 00000000..3d29ae42 --- /dev/null +++ b/tools/phylo_clustering/r_clustering.Rmd @@ -0,0 +1,234 @@ +--- +output: html_document +params: + data: + value: x + varExp: + value: x + method: + value: x +--- + + + + + + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` +

FROGS Phyloseq: Sample clustering using different linkage method

+ + Phyloseq `r packageVersion("phyloseq")` + +```{r include=FALSE, echo=FALSE} +library(phyloseq) +library(scales) +library(ape) +load(params$data) + +##get dist object from distance matrix file +#setwd(dirname(params$method)) +A <- read.table(file=params$method, row.names=1) +dist <- as.dist(A) + +## Env types +var <- get_variable(data, params$varExp) + +palette <- hue_pal()(length(levels(var))) # Automatic color palette: one color per different sample type + +tipColor <- col_factor(palette, levels = levels(var))(var) # Map sample type to color +``` + +#{.tabset .tabset-fade .tabset-pills} + +##Ward D2 +```{r, fig.width=8, fig.height=6, echo=FALSE} +clust.wardD2 <- as.phylo(hclust(dist, method = 'ward.D2')) +par(mfcol = c(1,1)) +plot(clust.wardD2, tip.color = tipColor, direction = "downwards", main = "Sample Clustering with Ward.D2 linkage") +``` +
+ + +##Complete +```{r, fig.width=8, fig.height=6, echo=FALSE} +clust.complete <- as.phylo(hclust(dist, method = 'complete')) +par(mfcol = c(1,1)) +plot(clust.complete, tip.color = tipColor, direction = "downwards", main = "Sample Clustering with Complete linkage") +``` +
+ + +##Single +```{r, fig.width=8, fig.height=6, echo=FALSE} +clust.single <- as.phylo(hclust(dist, method = 'single')) +par(mfcol = c(1,1)) +plot(clust.single, tip.color = tipColor, direction = "downwards", main = "Sample Clustering with Single linkage") +``` +
+ + +##R code + +

Loading packages & data

+```{r, eval=FALSE} +library(scales) +library(ape) +#if in new session +#library(phyloseq) +#data <- path to Rdata file +#load(data) + +##get dist object from distance matrix file +method <- # path to Beta diversity tsv file +A <- read.table(file=method, row.names=1) +dist <- as.dist(A) + +## Env types +varExp <- #Experiment variable to split plot +var <- get_variable(data,varExp) +``` + +

Make color palettes

+```{r, eval=FALSE} +# automatic color palette: one color per different sample type +palette <- hue_pal()(length(levels(var))) +# Map sample type to color +tipColor <- col_factor(palette, levels = levels(var))(var) +``` + +

Sample clustering using different linkage method

+```{r, eval=FALSE} +clust.wardD2 <- as.phylo(hclust(dist, method = 'ward.D2')) +par(mfcol = c(1,1)) +plot(clust.wardD2, tip.color = tipColor, direction = "downwards", main = "Sample Clustering with Ward.D2 linkage") + +clust.complete <- as.phylo(hclust(dist, method = 'complete')) +par(mfcol = c(1,1)) +plot(clust.complete, tip.color = tipColor, direction = "downwards", main = "Sample Clustering with Complete linkage") + +clust.single <- as.phylo(hclust(dist, method = 'single')) +par(mfcol = c(1,1)) +plot(clust.single, tip.color = tipColor, direction = "downwards", main = "Sample Clustering with Single linkage") +``` + + + + + + + diff --git a/tools/phylo_clustering/r_clustering.py b/tools/phylo_clustering/r_clustering.py new file mode 100755 index 00000000..f3fb7c41 --- /dev/null +++ b/tools/phylo_clustering/r_clustering.py @@ -0,0 +1,100 @@ +#!/usr/bin/env python2.7 +# +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +# +__author__ = 'Ta Thi Ngan & Maria Bernard INRA - SIGENAE' +__copyright__ = 'Copyright (C) 2017 INRA' +__license__ = 'GNU General Public License' +__version__ = '1.0.0' +__email__ = 'frogs@toulouse.inra.fr' +__status__ = 'prod' + +import os +import sys +import argparse + +CURRENT_DIR = os.path.dirname(os.path.abspath(__file__)) +# PATH +BIN_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "libexec")) +os.environ['PATH'] = BIN_DIR + os.pathsep + os.environ['PATH'] +# PYTHONPATH +LIB_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "lib")) +sys.path.append(LIB_DIR) +if os.getenv('PYTHONPATH') is None: os.environ['PYTHONPATH'] = LIB_DIR +else: os.environ['PYTHONPATH'] = os.environ['PYTHONPATH'] + os.pathsep + LIB_DIR + +from frogsUtils import * +################################################################################################################################################## +# +# COMMAND LINES +# +################################################################################################################################################## + +class Rscript(Cmd): + """ + @summary: Launch Rmarkdown script to clustering of samples (from beta diversity distances) using different linkage method. + @see: http://rmarkdown.rstudio.com/ + https://joey711.github.io/phyloseq/ + @return: the html file containing the clustering plot. + """ + def __init__(self, html, data, varExp, method): + """ + @params html: [str] Path to store resulting html file. + @param data: [str] One phyloseq object in Rdata file, the result of FROGS Phyloseq Import Data. + @param varExp: [str] The experiment variable. + @param method: [str] Path of data file containing beta diversity distance matrix. These file is the result of FROGS Phyloseq Beta Diversity. + """ + rmd = os.path.join(CURRENT_DIR, "r_clustering.Rmd") + Cmd.__init__( self, + 'Rscript', + 'Run 1 code Rmarkdown', + '-e "rmarkdown::render('+"'"+rmd+"',output_file='"+html+"', params=list(data='"+data+"', varExp='"+varExp+"',method='"+method+"'), intermediates_dir='"+os.path.dirname(html)+"')"+'" 2> /dev/null', + "-e '(sessionInfo()[[1]][13])[[1]][1]; paste(\"Rmarkdown version: \",packageVersion(\"rmarkdown\")) ; library(phyloseq); paste(\"Phyloseq version: \",packageVersion(\"phyloseq\"))'") + def get_version(self): + """ + @summary: Returns the program version number. + @return: [str] Version number if this is possible, otherwise this method return 'unknown'. + """ + return Cmd.get_version(self, 'stdout') + +################################################################################################################################################## +# +# MAIN +# +################################################################################################################################################## + +if __name__ == "__main__": + + # Manage parameters + parser = argparse.ArgumentParser( description='Clustering of samples using different linkage method.' ) + parser.add_argument('-v', '--varExp', type=str, required=True, default=None, help='The experiment variable you want to analyse.') + # Inputs + group_input = parser.add_argument_group( 'Inputs' ) + group_input.add_argument('-d','--data', required=True, default=None, help="The path of RData file containing a phyloseq object-the result of FROGS Phyloseq Import Data" ) + group_input.add_argument('-m','--method', required=True, default=None, help="The path of data file containing beta diversity distance matrix. These file is the result of FROGS Phyloseq Beta Diversity." ) + + # output + group_output = parser.add_argument_group( 'Outputs' ) + group_output.add_argument('-o','--html', default='clustering.html', help="The path to store resulting html file. [Default: %(default)s]" ) + group_output.add_argument( '-l', '--log_file', default=sys.stdout, help='This output file will contain several information on executed commands.') + args = parser.parse_args() + prevent_shell_injections(args) + # Process + Logger.static_write(args.log_file, "## Application\nSoftware :" + sys.argv[0] + " (version : " + str(__version__) + ")\nCommand : " + " ".join(sys.argv) + "\n\n") + html=os.path.abspath(args.html) + data=os.path.abspath(args.data) + method=os.path.abspath(args.method) + Rscript(html, data, args.varExp, method).submit( args.log_file ) diff --git a/tools/phylo_clustering/r_clustering.xml b/tools/phylo_clustering/r_clustering.xml new file mode 100755 index 00000000..daac13fe --- /dev/null +++ b/tools/phylo_clustering/r_clustering.xml @@ -0,0 +1,96 @@ + + + + of samples using different linkage methods + r_clustering.py + --html $html + --data $data + --varExp $varExp + --method $method + + + + + + + + + + + + + + + + + + + +.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and customized R function, this tool contructs the clustering plot for cluster analysis with different linkage methods. + + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**data file** (format RData): +The informations of data in one phyloseq object. +This is the result of FROGS Phyloseq Import Data tool. + +**distance file** (format tabular): +The data file containing beta diversity distance matrix. +This file is the result of FROGS Phyloseq Beta Diversity tool. + +.. class:: h3 + +Output + +**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): + +.. container:: row + + .. image:: ${static_path}/images/tools/frogs/phyloseq_clustering_ward.png + :height: 576 + :width: 768 + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@toulouse.inra.fr + +Repository: https://github.com/geraldinepascal/FROGS + +Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf + +Depending on the help provided you can cite us in acknowledgements, references or both. + + + diff --git a/tools/phylo_clustering/test.sh b/tools/phylo_clustering/test.sh new file mode 100755 index 00000000..4bca0190 --- /dev/null +++ b/tools/phylo_clustering/test.sh @@ -0,0 +1,17 @@ +#!/bin/sh +export PATH=../../libexec:$PATH +export PYTHONPATH=../../lib:$PYTHONPATH + +if [ -d test ] +then + rm -r test/* +else + mkdir test +fi + +python r_clustering.py \ + --data data/data.Rdata \ + --varExp EnvType \ + --method data/Unifrac.tsv \ + --html test/phylo_clustering.html \ + -l test/phylo_clustering.log diff --git a/tools/phylo_composition/data/data.Rdata b/tools/phylo_composition/data/data.Rdata new file mode 100644 index 00000000..aca7595e Binary files /dev/null and b/tools/phylo_composition/data/data.Rdata differ diff --git a/tools/phylo_composition/r_composition.Rmd b/tools/phylo_composition/r_composition.Rmd new file mode 100755 index 00000000..e9b57564 --- /dev/null +++ b/tools/phylo_composition/r_composition.Rmd @@ -0,0 +1,166 @@ +--- +output: + html_document +params: + data: + value: x + varExp: + value: x + taxaRank1: + value: x + taxaSet1: + value: x + taxaRank2: + value: x + numberOfTaxa: + value: x +--- + + + + + + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` +

FROGS Phyloseq: Visualize Data Composition

+ + Phyloseq `r packageVersion("phyloseq")` + +```{r, include=FALSE, cache=FALSE, warning=FALSE} +library(plotly) +source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R") +load(params$data) +``` + +#{.tabset .tabset-fade .tabset-pills} +##Bar plot +```{r, fig.width=10, fig.height=8, echo=FALSE, comment=NA, cache=FALSE} +e <- paste('facet_wrap(~', params$varExp,', scales = "free_x", nrow = 1)') +p <- plot_bar(data,fill= params$taxaRank2) + eval(parse(text = e)) + ggtitle(paste("Bar plot colored by", params$taxaRank2))+ theme(plot.title = element_text(hjust = 0.5)) +plot(p) +``` +
+ + +##Composition plot +```{r, echo=FALSE, comment=NA, cache=FALSE, warning=FALSE, include=FALSE} +taxaSet1 <- unlist(strsplit(params$taxaSet1, " ")) +p <- plot_composition(data, params$taxaRank1, taxaSet1, params$taxaRank2, params$numberOfTaxa, fill=params$taxaRank2) +p <- p + eval(parse(text = e)) + theme(plot.title = element_text(hjust = 0.5)) +gp <- ggplotly(p) +``` +```{r, fig.width=10, fig.height=8, echo=FALSE, comment=NA, cache=FALSE, warning=FALSE} +gp$x$layout$annotations[[1]]$x <- -0.08 +gp$x$layout$margin$l = 75 +gp$x$layout$margin$b = 100 +gp$x$layout$margin$t = 100 +gp +``` + +##R code +

Loading packages & data

+```{r, eval=FALSE} +library(plotly) +source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R") +#if in new session +#data <- path to Rdata file +#load(data) +``` + +

Bar plot

+```{r, comment=NA, cache=FALSE, echo=FALSE} +taxaSet1 <- paste0("c(\"", paste(unlist(strsplit(params$taxaSet1, " ")), collapse = "\", \""), "\")") +cat(paste(sep = "","p <- plot_bar(data,fill=", '"', params$taxaRank2, '"', ") + facet_wrap(~", params$varExp, ', scales = "free_x", nrow = 1) + ggtitle("', paste("Bar plot colored by", params$taxaRank2, '")'), '+ theme(plot.title = element_text(hjust = 0.5))', '\nplot(p)')) +``` + +

Composition plot

+```{r, comment=NA, cache=FALSE, echo=FALSE} +cat(paste(sep = "",'taxaSet1 <- unlist(strsplit(', params$taxaSet1, ', " "))\n', "p <- plot_composition(data,", '"', params$taxaRank1, '" ,taxaSet1 , "', params$taxaRank2, '" ,', params$numberOfTaxa, ', fill="', params$taxaRank2, '"', ") + eval(", parse(text = e),")"),'+ theme(plot.title = element_text(hjust = 0.5))', '\nggplotly(p)') +``` + + + + + + + diff --git a/tools/phylo_composition/r_composition.py b/tools/phylo_composition/r_composition.py new file mode 100755 index 00000000..09ca726b --- /dev/null +++ b/tools/phylo_composition/r_composition.py @@ -0,0 +1,107 @@ +#!/usr/bin/env python2.7 +# +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +# +__author__ = ' Ta Thi Ngan & Maria Bernard INRA - SIGENAE ' +__copyright__ = 'Copyright (C) 2017 INRA' +__license__ = 'GNU General Public License' +__version__ = '1.0.0' +__email__ = 'frogs@toulouse.inra.fr' +__status__ = 'prod' + +import os +import sys +import argparse + +CURRENT_DIR = os.path.dirname(os.path.abspath(__file__)) +# PATH +BIN_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "libexec")) +os.environ['PATH'] = BIN_DIR + os.pathsep + os.environ['PATH'] +# PYTHONPATH +LIB_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "lib")) +sys.path.append(LIB_DIR) +if os.getenv('PYTHONPATH') is None: os.environ['PYTHONPATH'] = LIB_DIR +else: os.environ['PYTHONPATH'] = os.environ['PYTHONPATH'] + os.pathsep + LIB_DIR + +from frogsUtils import * +################################################################################################################################################## +# +# COMMAND LINES +# +################################################################################################################################################## + +class Rscript(Cmd): + """ + @summary: Launch Rmarkdown script to present the composition of data with package phyloseq + @see: http://rmarkdown.rstudio.com/ + https://joey711.github.io/phyloseq/ + @return: bar plot and composition plot in one html file. + """ + def __init__(self, html, data, varExp,taxaRank1,taxaSet1,taxaRank2,numberOfTaxa): + """ + @param html: [str] path to store resulting html file. + @param data: [str] path to phyloseq object in RData file, the result of FROGS Phyloseq Import Data. + @param varExp: [str] The experiment variable used to split plot. + @param taxaRank1: [str] Taxonomic rank name to subset your data. + @param taxaSet1: [str] The taxon name among taxaRank1 to subset your data. + @param taxaRank2: [str] The sub taxonomic rank name to aggregate your data. + @param numberOfTaxa: [str] The number of the most abundant taxa to keep at level taxaRank2. + """ + rmd = os.path.join(CURRENT_DIR, "r_composition.Rmd") + Cmd.__init__( self, + 'Rscript', + 'Run 1 code Rmarkdown', + '-e "rmarkdown::render('+"'"+rmd+"',output_file='"+html+"', params=list(data='"+data+"', varExp='"+varExp+"',taxaRank1='"+taxaRank1+"',taxaSet1='"+taxaSet1+"',taxaRank2='"+taxaRank2+"',numberOfTaxa="+str(numberOfTaxa)+"), intermediates_dir='"+os.path.dirname(html)+"')"+'" 2> /dev/null', + "-e '(sessionInfo()[[1]][13])[[1]][1]; paste(\"Rmarkdown version: \",packageVersion(\"rmarkdown\")) ; library(phyloseq); paste(\"Phyloseq version: \",packageVersion(\"phyloseq\"))'") + def get_version(self): + """ + @summary: Returns the program version number. + @return: [str] Version number if this is possible, otherwise this method return 'unknown'. + """ + return Cmd.get_version(self, 'stdout') + +################################################################################################################################################## +# +# MAIN +# +################################################################################################################################################## + +if __name__ == "__main__": + + # Manage parameters + parser = argparse.ArgumentParser( description='Present the composition of data with package phyloseq' ) + parser.add_argument('-v', '--varExp', type=str, required=True, help='The experiment variable used to split plot.' ) + parser.add_argument('-r1', '--taxaRank1', type=str, required=True, help='Select taxonomic rank name to subset your data. [ex: Kingdom]' ) + parser.add_argument('-s1', '--taxaSet1', type=str ,nargs='*', required=True, help='Select taxon name among taxaRank1 to subset your data. [ex: Bacteria]' ) + parser.add_argument('-r2', '--taxaRank2', type=str,required=True, help='Select sub taxonomic rank name to aggregate your data. [ex: Phylum]" ' ) + parser.add_argument('-n', '--numberOfTaxa', type=int, required=True, help='The number of the most abundant taxa to keep at taxaRank2. [ex: 9]" ' ) + + # Inputs + group_input = parser.add_argument_group( 'Inputs' ) + group_input.add_argument('-d','--data', required=True, default=None, help="The path of RData file containing a phyloseq object-the result of FROGS Phyloseq Import Data") + + # output + group_output = parser.add_argument_group( 'Outputs' ) + group_output.add_argument('-o','--html', default='composition.html', help="The path to store resulting html file. [Default: %(default)s]" ) + group_output.add_argument( '-l', '--log_file', default=sys.stdout, help='This output file will contain several information on executed commands.') + args = parser.parse_args() + prevent_shell_injections(args) + # Process + Logger.static_write(args.log_file, "## Application\nSoftware :" + sys.argv[0] + " (version : " + str(__version__) + ")\nCommand : " + " ".join(sys.argv) + "\n\n") + html=os.path.abspath(args.html) + data=os.path.abspath(args.data) + taxaSet1=" ".join(args.taxaSet1) + Rscript(html, data, args.varExp, args.taxaRank1, str(taxaSet1), args.taxaRank2, args.numberOfTaxa).submit( args.log_file ) diff --git a/tools/phylo_composition/r_composition.xml b/tools/phylo_composition/r_composition.xml new file mode 100755 index 00000000..02575447 --- /dev/null +++ b/tools/phylo_composition/r_composition.xml @@ -0,0 +1,120 @@ + + + + with bar plot and composition plot + r_composition.py + --data $data + --varExp $varExp + --taxaRank1 $taxaRank1 + --taxaSet1 $taxaSet1 + --taxaRank2 $taxaRank2 + --numberOfTaxa $numberOfTaxa + --html $html + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and custom R function, this tool constructs two plots to visualise the sample composition: one at the OTU level and another one at the specified aggregation level (*e.g.* Phylum) after keeping only a subset of taxa (*e.g.* Bacteria at the level Kingdom). It helps answer the question: "What is the composition at the Phylum level within Bacteria?". By default, the plot exhibits only the abundance of the 9 most abundant taxa (as specified). In general, the representation of more than 10 taxa is hard to read on plots. + + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**data file** (format rdata): +One phyloseq object containing the OTU abundance table, their taxonomies and optionnaly a phylogenetic tree, and the sample experiment metadata. +this file is the result of FROGS Phyloseq Import Data tool. + +.. class:: h3 + +Output + +**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): data composition plots. + +Bar plot of OTUs is colored with aggregated taxonomic level *i.e* "Phylum" : + + .. image:: ${static_path}/images/tools/frogs/phyloseq_bar_plot.png + :height: 646 + :width: 800 + +Composition plot: plot the most abundant sub taxonomic level among a selection of OTUs. + +- Selection of OTUs: + + - Taxonomic level name to subset: Kingdom + - Taxon name: Bacteria + +- Aggregation of OTUs : + + - Taxonomic level used to agglomerate: Phylum + +- Number of the most abundant taxa to keep: 5 + + .. image:: ${static_path}/images/tools/frogs/phyloseq_composition_plot.png + :height: 644 + :width: 800 + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@toulouse.inra.fr + +Repository: https://github.com/geraldinepascal/FROGS + +Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf + +Depending on the help provided you can cite us in acknowledgements, references or both. + + + diff --git a/tools/phylo_composition/test.sh b/tools/phylo_composition/test.sh new file mode 100755 index 00000000..4b463cab --- /dev/null +++ b/tools/phylo_composition/test.sh @@ -0,0 +1,14 @@ +#!/bin/sh +export PATH=../../libexec:$PATH +export PYTHONPATH=../../lib:$PYTHONPATH + +if [ -d test ] +then + rm -r test/* +else + mkdir test +fi + +python2.7 r_composition.py -d data/data.Rdata \ + -v EnvType -r1 Kingdom -s1 Bacteria -r2 Phylum -n 9 \ + -l test/phylo_compo.log -o test/phylo_compo.html diff --git a/tools/phylo_import/data/chaillou.biom b/tools/phylo_import/data/chaillou.biom new file mode 100755 index 00000000..c00f819f --- /dev/null +++ b/tools/phylo_import/data/chaillou.biom @@ -0,0 +1 @@ +{"rows": [{"id": "otu_01778", "metadata": {"taxonomy": ["k__Bacteria", "p__Tenericutes", "c__Mollicutes", "o__Mycoplasmatales", "f__Mycoplasmataceae", "g__Candidatus Lumbricincola", "s__NA"]}}, {"id": "otu_01838", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Prevotellaceae", "g__Prevotella", "s__NA"]}}, {"id": "otu_01386", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Xanthomonadales", "f__Xanthomonadaceae", "g__Dyella", "s__Ginsengisoli"]}}, {"id": "otu_01835", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Planococcaceae", "g__Incertae Sedis", "s__NA"]}}, {"id": "otu_01837", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Flavobacteria", "o__Flavobacteriales", "f__Flavobacteriaceae", "g__Flavobacterium", "s__NA"]}}, {"id": "otu_01832", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Leuconostocaceae", "g__Weissella", "s__NA"]}}, {"id": "otu_01833", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Actinomycetales", "f__Actinomycetaceae", "g__Actinomyces", "s__NA"]}}, {"id": "otu_00156", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Micrococcales", "f__Brevibacteriaceae", "g__Brevibacterium", "s__Marinum"]}}, {"id": "otu_01719", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Betaproteobacteria", "o__Neisseriales", "f__Neisseriaceae", "g__Neisseria", "s__Perflava"]}}, {"id": "otu_00015", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Aerococcaceae", "g__Facklamia", "s__Tabacinasalis"]}}, {"id": "otu_00769", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Lactobacillaceae", "g__Lactobacillus", "s__Sakei"]}}, {"id": "otu_00768", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Lactobacillaceae", "g__Lactobacillus", "s__Brevis"]}}, {"id": "otu_00011", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Acinetobacter", "s__Soli"]}}, {"id": "otu_00010", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Acinetobacter", "s__Junii"]}}, {"id": "otu_00013", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Acinetobacter", "s__Kyonggiensis"]}}, {"id": "otu_00012", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Acinetobacter", "s__Johnsonii"]}}, {"id": "otu_00018", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Aerococcaceae", "g__Abiotrophia", "s__Defectiva"]}}, {"id": "otu_00569", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Serratia", "s__Proteamaculans"]}}, {"id": "otu_00568", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Serratia", "s__Fonticola"]}}, {"id": "otu_00602", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Family XII Incertae Sedis", "g__Exiguobacterium", "s__Aestuarii"]}}, {"id": "otu_00386", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Betaproteobacteria", "o__Burkholderiales", "f__Comamonadaceae", "g__Comamonas", "s__Aquatica"]}}, {"id": "otu_00604", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Family XII Incertae Sedis", "g__Exiguobacterium", "s__Sibiricum"]}}, {"id": "otu_00605", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Family XII Incertae Sedis", "g__Exiguobacterium", "s__Undae"]}}, {"id": "otu_00607", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Family XII Incertae Sedis", "g__Exiguobacterium", "s__Indicum"]}}, {"id": "otu_00608", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Family XII Incertae Sedis", "g__Exiguobacterium", "s__Acetylicum"]}}, {"id": "otu_00566", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Serratia", "s__Liquefaciens"]}}, {"id": "otu_01849", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Flavobacteria", "o__Flavobacteriales", "f__Flavobacteriaceae", "g__Flavobacterium", "s__NA"]}}, {"id": "otu_01658", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Alphaproteobacteria", "o__Rhodobacterales", "f__Rhodobacteraceae", "g__Roseicyclus", "s__NA"]}}, {"id": "otu_01790", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Planococcaceae", "g__Jeotgalibacillus", "s__Psychrophilus"]}}, {"id": "otu_01841", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Family XI Incertae Sedis", "g__Gallicola", "s__NA"]}}, {"id": "otu_01840", "metadata": {"taxonomy": ["k__Bacteria", "p__Spirochaetes", "c__Spirochaetes", "o__Spirochaetales", "f__NA", "g__NA", "s__NA"]}}, {"id": "otu_01843", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Eubacteriaceae", "g__Eubacterium", "s__NA"]}}, {"id": "otu_01330", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Rhizobiaceae", "g__Rhizobium", "s__Fluminensis"]}}, {"id": "otu_01845", "metadata": {"taxonomy": ["k__Bacteria", "p__Tenericutes", "c__Mollicutes", "o__Mycoplasmatales", "f__Mycoplasmataceae", "g__Mycoplasma", "s__NA"]}}, {"id": "otu_01336", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Rhizobiaceae", "g__Rhizobium", "s__Daejeonense"]}}, {"id": "otu_01847", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae", "g__NA", "s__NA"]}}, {"id": "otu_01334", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Methylocystaceae", "g__Pleomorphomonas", "s__Oryzae"]}}, {"id": "otu_01487", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Sphingobacteria", "o__Sphingobacteriales", "f__Sphingobacteriaceae", "g__Sphingobacterium", "s__Faecium"]}}, {"id": "otu_01795", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Flavobacteria", "o__Flavobacteriales", "f__Flavobacteriaceae", "g__Flavobacterium", "s__NA"]}}, {"id": "otu_00127", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Prevotellaceae", "g__Prevotella", "s__Heparinolytica"]}}, {"id": "otu_01649", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Prevotellaceae", "g__Prevotella", "s__NA"]}}, {"id": "otu_01648", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Peptostreptococcaceae", "g__Peptostreptococcus", "s__NA"]}}, {"id": "otu_01647", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__NA", "g__NA", "s__NA"]}}, {"id": "otu_01645", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__BS11 gut group", "g__NA", "s__NA"]}}, {"id": "otu_01643", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Ruminococcaceae", "g__uncultured", "s__NA"]}}, {"id": "otu_01642", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Eubacteriaceae", "g__Eubacterium", "s__Rectale"]}}, {"id": "otu_01641", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Streptococcaceae", "g__Streptococcus", "s__Parasanguinis"]}}, {"id": "otu_00903", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Micrococcales", "f__Microbacteriaceae", "g__Pseudoclavibacter", "s__Helvolus"]}}, {"id": "otu_00462", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Corynebacteriales", "f__Corynebacteriaceae", "g__Corynebacterium", "s__Singulare"]}}, {"id": "otu_00469", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Corynebacteriales", "f__Corynebacteriaceae", "g__Corynebacterium", "s__Testudinoris"]}}, {"id": "otu_00263", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Clostridiaceae", "g__Clostridium", "s__Hastiforme"]}}, {"id": "otu_00260", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Clostridiaceae", "g__Clostridium", "s__Bartlettii"]}}, {"id": "otu_00266", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Clostridiaceae", "g__Clostridium", "s__Oroticum"]}}, {"id": "otu_01209", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Psychrobacter", "s__Nivimaris"]}}, {"id": "otu_01208", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Psychrobacter", "s__Faecalis"]}}, {"id": "otu_01205", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Pseudomonadaceae", "g__Pseudomonas", "s__Deceptionensis"]}}, {"id": "otu_01204", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Pseudomonadaceae", "g__Pseudomonas", "s__Fragi"]}}, {"id": "otu_01203", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Pseudomonadaceae", "g__Pseudomonas", "s__Fluorescens"]}}, {"id": "otu_00833", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Listeriaceae", "g__Listeria", "s__Monocytogenes"]}}, {"id": "otu_00838", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Staphylococcaceae", "g__Macrococcus", "s__Caseolyticus"]}}, {"id": "otu_01907", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Flavobacteria", "o__Flavobacteriales", "f__Flavobacteriaceae", "g__Chryseobacterium", "s__NA"]}}, {"id": "otu_00990", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Micrococcales", "f__Micrococcaceae", "g__Arthrobacter", "s__Antarcticus"]}}, {"id": "otu_00994", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Micrococcales", "f__Micrococcaceae", "g__Arthrobacter", "s__Psychrolactophilus"]}}, {"id": "otu_01025", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Betaproteobacteria", "o__Neisseriales", "f__Neisseriaceae", "g__Neisseria", "s__Subflava"]}}, {"id": "otu_00999", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Micrococcales", "f__Micrococcaceae", "g__Arthrobacter", "s__Cryotolerans"]}}, {"id": "otu_00411", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Betaproteobacteria", "o__Burkholderiales", "f__Comamonadaceae", "g__Simplicispira", "s__Psychrophila"]}}, {"id": "otu_00417", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Betaproteobacteria", "o__Burkholderiales", "f__Comamonadaceae", "g__Acidovorax", "s__Defluvii"]}}, {"id": "otu_00418", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Betaproteobacteria", "o__Burkholderiales", "f__Comamonadaceae", "g__Limnohabitans", "s__Planktonicus"]}}, {"id": "otu_00396", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Betaproteobacteria", "o__Burkholderiales", "f__Comamonadaceae", "g__Rhodoferax", "s__Ferrireducens"]}}, {"id": "otu_00391", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Betaproteobacteria", "o__Burkholderiales", "f__Comamonadaceae", "g__Polaromonas", "s__Hydrogenivorans"]}}, {"id": "otu_00398", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Betaproteobacteria", "o__Burkholderiales", "f__Comamonadaceae", "g__Acidovorax", "s__Temperans"]}}, {"id": "otu_00182", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Betaproteobacteria", "o__Burkholderiales", "f__Burkholderiaceae", "g__Ralstonia", "s__Pickettii"]}}, {"id": "otu_00191", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Carnobacteriaceae", "g__Carnobacterium", "s__Maltaromaticum"]}}, {"id": "otu_00192", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Carnobacteriaceae", "g__Carnobacterium", "s__Jeotgali"]}}, {"id": "otu_00193", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Carnobacteriaceae", "g__Carnobacterium", "s__Viridans"]}}, {"id": "otu_00194", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Carnobacteriaceae", "g__Carnobacterium", "s__Mobile"]}}, {"id": "otu_00195", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Lactobacillales", "f__Carnobacteriaceae", "g__Carnobacterium", "s__Inhibens"]}}, {"id": "otu_01737", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Sphingobacteria", "o__Sphingobacteriales", "f__Chitinophagaceae", "g__Sediminibacterium", "s__NA"]}}, {"id": "otu_01735", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Micrococcales", "f__Dermacoccaceae", "g__Dermacoccus", "s__Nishinomiyaensis"]}}, {"id": "otu_01734", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Betaproteobacteria", "o__Burkholderiales", "f__Comamonadaceae", "g__Acidovorax", "s__NA"]}}, {"id": "otu_01732", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Pseudomonadales", "f__Moraxellaceae", "g__Acinetobacter", "s__Schindleri"]}}, {"id": "otu_01731", "metadata": {"taxonomy": ["k__Bacteria", "p__Bacteroidetes", "c__Flavobacteria", "o__Flavobacteriales", "f__Flavobacteriaceae", "g__Cloacibacterium", "s__Normanense"]}}, {"id": "otu_00601", "metadata": {"taxonomy": ["k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Family XII Incertae Sedis", "g__Exiguobacterium", "s__Oxidotolerans"]}}, {"id": "otu_00527", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Morganella", "s__Psychrotolerans"]}}, {"id": "otu_00526", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Proteus", "s__Mirabilis"]}}, {"id": "otu_00521", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Morganella", "s__Morganii"]}}, {"id": "otu_00520", "metadata": {"taxonomy": ["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Raoultella", "s__Ornithinolytica"]}}, {"id": "otu_00482", "metadata": {"taxonomy": ["k__Bacteria", "p__Actinobacteria", "c__Actinobacteria", "o__Corynebacteriales", "f__Corynebacteriaceae", "g__Corynebacterium", "s__Ammoniagenes"]}}, 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Seafood +FST0.LOT08 FiletSaumon LOT8 Seafood +FST0.LOT10 FiletSaumon LOT10 Seafood +FCT0.LOT01 FiletCabillaud LOT1 Seafood +FCT0.LOT02 FiletCabillaud LOT2 Seafood +FCT0.LOT03 FiletCabillaud LOT3 Seafood +FCT0.LOT05 FiletCabillaud LOT5 Seafood +FCT0.LOT06 FiletCabillaud LOT6 Seafood +FCT0.LOT07 FiletCabillaud LOT7 Seafood +FCT0.LOT08 FiletCabillaud LOT8 Seafood +FCT0.LOT10 FiletCabillaud LOT10 Seafood +CDT0.LOT02 Crevette LOT2 Seafood +CDT0.LOT04 Crevette LOT4 Seafood +CDT0.LOT05 Crevette LOT5 Seafood +CDT0.LOT06 Crevette LOT6 Seafood +CDT0.LOT07 Crevette LOT7 Seafood +CDT0.LOT08 Crevette LOT8 Seafood +CDT0.LOT09 Crevette LOT9 Seafood +CDT0.LOT10 Crevette LOT10 Seafood diff --git a/tools/phylo_import/data/tree.nwk b/tools/phylo_import/data/tree.nwk new file mode 100755 index 00000000..d9b11cc9 --- /dev/null +++ b/tools/phylo_import/data/tree.nwk @@ -0,0 +1 @@ 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diff --git a/tools/phylo_import/r_import_data.Rmd b/tools/phylo_import/r_import_data.Rmd new file mode 100755 index 00000000..37c31bc4 --- /dev/null +++ b/tools/phylo_import/r_import_data.Rmd @@ -0,0 +1,286 @@ +--- +output: html_document +params: + biomfile: + value: x + samplefile: + value: x + treefile: + value: x + normalization: + value: x + outputRdata: + value: x + ranks : + value: x +--- + + + + + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +knitr::opts_chunk$set(error = TRUE) +``` +

FROGS Phyloseq: Import Data

+ + Phyloseq `r packageVersion("phyloseq")` + +```{r include=FALSE, cache=FALSE} +library(phyloseq) +library(ggplot2) +#library(biom) +library(ape) + +## import data +biomfile <- params$biomfile +data <- import_biom(biomfile) +tax <- tax_table(data)[[1]] + +if ((gregexpr('k__', tax))[[1]][1]>0) { + data <- import_biom(biomfile, parseFunction = parse_taxonomy_greengenes) +} else { +## change taxonomic rank names + new_rank <- as.list(strsplit(params$ranks, " ")[[1]]) + colnames(tax_table(data)) <- new_rank +} + +sampledata <- try(read.csv(params$samplefile, sep = "", row.names = 1), TRUE) +if (inherits(sampledata, "try-error") || ncol(sampledata)==0) { + sampledata <- read.csv(params$samplefile, sep = "\t", row.names = 1) +} + +sample_data(data) <- sampledata + +if (params$treefile!="None"){ + treefile <- read.tree(params$treefile) + phy_tree(data) <- treefile +} + +## levels order as input sample_data file +for ( variable in sample_variables(data)){ + variable.order = as.vector(unique(sampledata[,variable])) + sample_data(data)[,variable] <- factor(get_variable(data, variable),levels=variable.order) +} + +## normalization +if(params$normalization){ data <- rarefy_even_depth(data, rngseed = 1121983)} + +## save data +save(data, file=params$outputRdata) +``` + +#{.tabset .tabset-fade .tabset-pills} +##Summary +```{r,cache=FALSE, echo=FALSE, comment=NA} +data +if(params$normalization){cat(paste('Sequence number in each sample after normalization: ', head(sample_sums(data))[[1]]))} +``` + +##Ranks Names +```{r,cache=FALSE, echo=FALSE, comment=NA} +if ((gregexpr('k__', tax))[[1]][1]>0) { + cat("Warning : Taxonomic affiliations come from Greengenes database, user specified ranks names are ignored.") +} +cat(paste('Rank names : ',paste(rank_names(data),collapse=', '))) +``` + +##Sample metadata +```{r,cache=FALSE, echo=FALSE, comment=NA} +variables <- sample_variables(data) +cat(paste('Sample variables: ', paste(variables, collapse=', ' ))) + +for (var in variables){ + cat(paste(var,': ',paste(levels(factor(get_variable(data, varName = var))),collapse=', '), '\n\n')) +} +``` + +##Plot tree +```{r, fig.width=10, fig.height=8, cache=FALSE, echo=FALSE, comment=NA} + +if(params$treefile!="None"){ + p <- plot_tree(data, color=rank_names(data)[2]) + ggtitle(paste("Phylogenetic tree colored by", rank_names(data)[2])) + theme(plot.title = element_text(hjust = 0.5)) + plot(p) +} + +if(params$treefile=="None"){ + cat("There is no phylogenetic tree in the object you have provided.") +} +``` + + + +##R code +

Loading packages

+```{r, eval=FALSE} +library(phyloseq) +library(ape) +library(ggplot2) +``` + +

Importing data

+```{r, eval=FALSE} +biomfile <- # path to biom file +treefile <- # path to newick file if possible +samplefile <- # path to sample tsv file +outputRdata <- # path to output Rdata file +normalization <- # TRUE or FALSE +ranks <- # ranks names, ex: ranks <- "Royaume Phylum Classe Ordre Famille Genre Espece" + +data <- import_biom(biomfile) +tax <- tax_table(data)[[1]] + +if ((gregexpr('k__', tax))[[1]][1]>0) { + data <-import_biom(biomfile, parseFunction = parse_taxonomy_greengenes) +} else { +## change taxonomic rank names + new_rank <- as.list(strsplit(ranks, " ")[[1]]) + colnames(tax_table(data)) <- new_rank +} +sampledata <- try(read.csv(samplefile, sep = "", row.names = 1), TRUE) +if (inherits(sampledata, "try-error") || ncol(sampledata)==0) { + sampledata <- read.csv(samplefile, sep = "\t", row.names = 1) +} + +sample_data(data) <- sampledata +treefile <- read.tree(treefile) #if have treefile +phy_tree(data) <- treefile + +# levels order as input sample_data file +for ( variable in sample_variables(data)){ + variable.order = as.vector(unique(sampledata[,variable])) + sample_data(data)[,variable] <- factor(get_variable(data, variable),levels=variable.order) +} + +# normalization +if(normalization) { + data <- rarefy_even_depth(data, rngseed = 1121983); + cat(paste('Sequence number in each sample after normalization: ', head(sample_sums(data))[[1]], "\n")) +} +``` + +

Saving data

+```{r, eval=FALSE} +save(data, file=outputRdata) +``` + +

Data view

+```{r, eval=FALSE} +data +## if have treefile +p <- plot_tree(data, color=rank_names(data)[2]) + ggtitle(paste("Phylogenetic tree colored by", rank_names(data)[2])) + theme(plot.title = element_text(hjust = 0.5)) +plot(p) +``` + + + + + + + + + diff --git a/tools/phylo_import/r_import_data.py b/tools/phylo_import/r_import_data.py new file mode 100755 index 00000000..4d784a93 --- /dev/null +++ b/tools/phylo_import/r_import_data.py @@ -0,0 +1,114 @@ +#!/usr/bin/env python2.7 +# +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +# +__author__ = ' Ta Thi Ngan & Maria Bernard INRA - SIGENAE ' +__copyright__ = 'Copyright (C) 2017 INRA' +__license__ = 'GNU General Public License' +__version__ = '1.0.0' +__email__ = 'frogs@toulouse.inra.fr' +__status__ = 'prod' + +import os +import sys +import argparse + +CURRENT_DIR = os.path.dirname(os.path.abspath(__file__)) +# PATH +BIN_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "libexec")) +os.environ['PATH'] = BIN_DIR + os.pathsep + os.environ['PATH'] +# PYTHONPATH +LIB_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "lib")) +sys.path.append(LIB_DIR) +if os.getenv('PYTHONPATH') is None: os.environ['PYTHONPATH'] = LIB_DIR +else: os.environ['PYTHONPATH'] = os.environ['PYTHONPATH'] + os.pathsep + LIB_DIR + +from frogsUtils import * +################################################################################################################################################## +# +# COMMAND LINES +# +################################################################################################################################################## + +class Rscript(Cmd): + """ + @summary: Launch Rmarkdown script to import data from three files: biomfile, samplefile, treefile into a phyloseq object. + @see: http://rmarkdown.rstudio.com/ + https://joey711.github.io/phyloseq/ + """ + def __init__(self, biomfile, samplefile, treefile, html, normalization, data, ranks): + """ + @param biomfile: [str] The biom file contains the OTU's informations: abundance and taxonomy. These file is the result of FROGS. + @param samplefile: [str] The tabular file contains the samples's informations. + Advice: within SampleID or without SampleID + @param treefile: [str] The Newick file contains the tree's informations from Frogs Tree. + @param html: [str] The path to store resulting html file. + @param normalization: [str] To normalize data before analysis. + @param data: [str] The path to store one phyloseq-class object in Rdata file. + @param ranks: [str] The ordered taxonomic ranks levels stored in BIOM. Each rank is separated by one space. + """ + rmd = os.path.join(CURRENT_DIR, "r_import_data.Rmd") + Cmd.__init__( self, + 'Rscript', + 'Run r_import_data.Rmd', + '-e "rmarkdown::render('+"'"+rmd+"',output_file='"+html+"', params=list(biomfile='"+biomfile+"', samplefile='"+samplefile+"', treefile='"+treefile+"', normalization="+normalization+", outputRdata='"+data+"', ranks='"+ranks+"'), intermediates_dir='"+os.path.dirname(html)+"')"+'" 2> /dev/null', + "-e '(sessionInfo()[[1]][13])[[1]][1]; paste(\"Rmarkdown version: \",packageVersion(\"rmarkdown\")) ; library(phyloseq); paste(\"Phyloseq version: \",packageVersion(\"phyloseq\"))'") + def get_version(self): + """ + @summary: Returns the program version number. + @return: [str] Version number if this is possible, otherwise this method return 'unknown'. + """ + return Cmd.get_version(self, 'stdout') + +################################################################################################################################################## +# +# MAIN +# +################################################################################################################################################## + +if __name__ == "__main__": + + # Manage parameters + parser = argparse.ArgumentParser( description='Launch Rmardown script to import data from 3 files: biomfile, samplefile, treefile into a phyloseq object') + parser.add_argument( '-n','--normalization', default=False, action='store_true', help='To normalize data before analysis. Use this option if you didnt do it in FROGS Abundance normalisation. [Default: %(default)s]') + parser.add_argument( '-r','--ranks', type=str, nargs='*', default=['Kingdom', 'Phylum', 'Class', 'Order','Family','Genus', 'Species'], help='The ordered taxonomic ranks levels stored in BIOM. Each rank is separated by one space. [Default: %(default)s]') + # Inputs + group_input = parser.add_argument_group( 'Inputs' ) + group_input.add_argument( '-b', '--biomfile', required=True, help='path to biom file (format: biom1). These file is the result of FROGS.' ) + group_input.add_argument( '-s', '--samplefile', required=True, help='path to sample file (format: tabular).' ) + group_input.add_argument( '-t', '--treefile', default=None, help='path to tree file from FROGS Tree (format: Newich "nhx" or "nwk" ).' ) + + # output + group_output = parser.add_argument_group( 'Outputs' ) + group_output.add_argument('-d','--data', default='phyloseq_data.Rdata', help="path to store phyloseq-class object in Rdata file. [Default: %(default)s]" ) + group_output.add_argument('-o','--html', default='summary.html', help="path to store resulting html file. [Default: %(default)s]" ) + group_output.add_argument( '-l', '--log_file', default=sys.stdout, help='This output file will contain several information on executed commands.') + args = parser.parse_args() + prevent_shell_injections(args) + + # Process + Logger.static_write(args.log_file, "## Application\nSoftware :" + sys.argv[0] + " (version : " + str(__version__) + ")\nCommand : " + " ".join(sys.argv) + "\n\n") + html=os.path.abspath(args.html) + data=os.path.abspath(args.data) + biomfile=os.path.abspath(args.biomfile) + samplefile=os.path.abspath(args.samplefile) + filename_treefile = ".".join(os.path.split(args.treefile)[1].split('.')[:-1]) + if (args.treefile is None) or (args.treefile =='None') or (filename_treefile == ""): + treefile="None" + else: + treefile=os.path.abspath(args.treefile) + ranks=" ".join(args.ranks) + Rscript(biomfile, samplefile, treefile, html, str(args.normalization).upper(), data, str(ranks)).submit(args.log_file) diff --git a/tools/phylo_import/r_import_data.xml b/tools/phylo_import/r_import_data.xml new file mode 100755 index 00000000..ae011359 --- /dev/null +++ b/tools/phylo_import/r_import_data.xml @@ -0,0 +1,119 @@ + + + + from 3 files: biomfile, samplefile, treefile + r_import_data.py --biomfile $biomfile + #if $samplefile + --samplefile $samplefile + #end if + --treefile $treefile + --ranks "$ranks" + #if $normalization + --normalization + #end if + --html $html + --data $data + + + + + + + + + + + + + + + + + + + + + + + +.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Launch Rmarkdown script to import data from 3 files: biomfile, samplefile, treefile into a `phyloseq <https://joey711.github.io/phyloseq/>`_ object. + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**OTU biom file**: + +The OTU biom file (format `biom1 <http://biom-format.org/documentation/format_versions/biom-1.0.html>`_). +This file is the result of FROGS. +The example of biom file: + + .. image:: ${static_path}/images/tools/frogs/biomfile.png + :height: 30 + :width: 733 + +**Newick file** (tree.nwk): + +Newick file (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_) is the result of FROGS Tree: + + .. image:: ${static_path}/images/tools/frogs/nwk_treefile.png + +**Sample file**: +The file contains the conditions of experiment with sample ID in the first column: + + .. image:: ${static_path}/images/tools/frogs/phyloseq_samplefile.png + :height: 115 + :width: 369 + +.. class:: h3 + +Output + +**Html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The summary of phyloseq object. + + .. image:: ${static_path}/images/tools/frogs/phyloseq_import_data_html.png + +**Data file** (format rdata): The informations of data in one phyloseq object. + + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@toulouse.inra.fr + +Repository: https://github.com/geraldinepascal/FROGS + +Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf + +Depending on the help provided you can cite us in acknowledgements, references or both. + + + diff --git a/tools/phylo_import/test.sh b/tools/phylo_import/test.sh new file mode 100755 index 00000000..ed78bd95 --- /dev/null +++ b/tools/phylo_import/test.sh @@ -0,0 +1,21 @@ +#!/bin/sh +export PATH=../../libexec:$PATH +export PYTHONPATH=../../lib:$PYTHONPATH + + +# Create output folder +if [ ! -d "test" ] +then + mkdir test +else + rm -r test/* +fi + +# without normalisation and default ranks +mkdir -p test/ +python r_import_data.py \ + -n \ + -b data/chaillou.biom \ + -s data/sample_data.tsv \ + -t data/tree.nwk \ + -d test/phylo_import.Rdata -o test/phylo_import.html -l test/phylo_import.log diff --git a/tools/phylo_manova/data/Unifrac.tsv b/tools/phylo_manova/data/Unifrac.tsv new file mode 100755 index 00000000..ae7b4cb6 --- /dev/null +++ b/tools/phylo_manova/data/Unifrac.tsv @@ 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0.407702954758623 0.366536918145145 0.278078263394802 0 diff --git a/tools/phylo_manova/data/data.Rdata b/tools/phylo_manova/data/data.Rdata new file mode 100755 index 00000000..aca7595e Binary files /dev/null and b/tools/phylo_manova/data/data.Rdata differ diff --git a/tools/phylo_manova/r_manova.Rmd b/tools/phylo_manova/r_manova.Rmd new file mode 100755 index 00000000..b56aef74 --- /dev/null +++ b/tools/phylo_manova/r_manova.Rmd @@ -0,0 +1,123 @@ +--- +output: html_document +params: + data: + value: x + varExp: + value: x + method: + value: x +--- + + + + + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` +

FROGS Phyloseq: Multivariate Analysis of Variance

+ + Phyloseq `r packageVersion("phyloseq")` + +```{r include=FALSE, echo=FALSE} +library(phyloseq) +library(vegan) +load(params$data) + +##get dist object from distance matrix file +setwd(dirname(params$method)) +A <- read.table(file=basename(params$method), row.names=1) +dist.a <- as.dist(A) +metadata <- as(sample_data(data), "data.frame") ## convert sample_data to data.frame +``` + +#{.tabset .tabset-fade .tabset-pills} +##Multivariate ANOVA performed with adonis +```{r, echo=FALSE, cach=FALSE, comment=NA} +adonis <- paste('adonis(dist.a ~ ', params$varExp, ', data = metadata, perm = 9999)') +eval(parse(text = adonis)) +``` + +##R code +

Loading packages & data

+```{r, eval=FALSE} +library(vegan) +## if in new session +# library(phyloseq) +# +## load phyloseq object +# data <- path to Rdata file +# load(data) +# extract sample metadata in a dataframe +metadata <- as(sample_data(data), "data.frame") + +## load beta distance matrix +beta_file <- # path to Beta diversity tsv file +A <- read.table(file=beta_file, row.names=1) +beta_dist <- as.dist(A) +``` +

With adonis

+```{r, comment=NA, cache=FALSE, echo=FALSE} +cat(paste(sep="","## change experiment variable (currently ", params$varExp, " )if you wish\n","## Multivariate ANOVA performed with adonis",'\nadonis(beta_dist ~ ', params$varExp, ', data = metadata, perm = 9999)')) +``` + + + + + diff --git a/tools/phylo_manova/r_manova.py b/tools/phylo_manova/r_manova.py new file mode 100755 index 00000000..3f8e0bcc --- /dev/null +++ b/tools/phylo_manova/r_manova.py @@ -0,0 +1,107 @@ +#!/usr/bin/env python2.7 +# +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +# +__author__ = 'Ta Thi Ngan & Maria Bernard INRA - SIGENAE' +__copyright__ = 'Copyright (C) 2017 INRA' +__license__ = 'GNU General Public License' +__version__ = '1.0.0' +__email__ = 'frogs@toulouse.inra.fr' +__status__ = 'prod' + +import os +import sys +import argparse +CURRENT_DIR = os.path.dirname(os.path.abspath(__file__)) +# PATH +BIN_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "libexec")) +os.environ['PATH'] = BIN_DIR + os.pathsep + os.environ['PATH'] +# PYTHONPATH +LIB_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "lib")) +sys.path.append(LIB_DIR) +if os.getenv('PYTHONPATH') is None: os.environ['PYTHONPATH'] = LIB_DIR +else: os.environ['PYTHONPATH'] = os.environ['PYTHONPATH'] + os.pathsep + LIB_DIR + +from frogsUtils import * +################################################################################################################################################## +# +# COMMAND LINES +# +################################################################################################################################################## + +class Rscript(Cmd): + """ + @summary: Launch Rmarkdown script to Multivariate Analysis of Variance (MANOVA) test with CAP (Canonical Analysis of Principal Coordinates) by adonis. + @see: http://rmarkdown.rstudio.com/ + https://joey711.github.io/phyloseq/ + @return: the html file containing manova test result. + """ + def __init__(self, html, data, varExp, matrix): + """ + @param html: [str] The path to store resulting html file. + @param data: [str] One phyloseq object in Rdata file, the result of FROGS Phyloseq Import Data. + @param varExp: [str] The experiment variable. + @param matrix: [str] Path of data file containing beta diversity distance matrix. These file is the result of FROGS Phyloseq Beta Diversity. + """ + rmd = os.path.join(CURRENT_DIR, "r_manova.Rmd") + Cmd.__init__( self, + 'Rscript', + 'Run 1 code Rmarkdown', + '-e "rmarkdown::render('+"'"+rmd+"',output_file='"+html+"', params=list(data='"+data+"', varExp='"+varExp+"',method='"+matrix+"'), intermediates_dir='"+os.path.dirname(html)+"')"+'" 2> /dev/null', + "-e '(sessionInfo()[[1]][13])[[1]][1]; paste(\"Rmarkdown version: \",packageVersion(\"rmarkdown\")) ; library(phyloseq); paste(\"Phyloseq version: \",packageVersion(\"phyloseq\"))'") + def get_version(self): + """ + @summary: Returns the program version number. + @return: [str] Version number if this is possible, otherwise this method return 'unknown'. + """ + return Cmd.get_version(self, 'stdout') + +################################################################################################################################################## +# +# MAIN +# +################################################################################################################################################## + +if __name__ == "__main__": + + # Manage parameters + parser = argparse.ArgumentParser( description='Multivariate Analysis of Variance (MANOVA) test with CAP (Canonical Analysis of Principal Coordinates) by adonis.' ) + parser.add_argument('-v', '--varExp', type=str, required=True, default=None, help='The experiment variable you want to analyse.') + + # Inputs + group_input = parser.add_argument_group( 'Inputs' ) + group_input.add_argument('-d','--data', required=True, default=None, help="The path of RData file containing a phyloseq object-the result of FROGS Phyloseq Import Data" ) + group_input.add_argument('-m','--distance-matrix', required=True, default=None, help="The path of data file containing beta diversity distance matrix. These file is the result of FROGS Phyloseq Beta Diversity." ) + + # output + group_output = parser.add_argument_group( 'Outputs' ) + group_output.add_argument('-o','--html', default='manova.html', help="The path to store resulting html file. [Default: %(default)s]" ) + group_output.add_argument( '-l', '--log_file', default=sys.stdout, help='This output file will contain several information on executed commands.') + + args = parser.parse_args() + prevent_shell_injections(args) + # Process + # keep quote around varExp + idx=sys.argv.index("--varExp")+1 + cmd = " ".join(sys.argv[0:idx]) + " \"" + sys.argv[idx] + "\" " + if idx != len(sys.argv): + cmd += " ".join(sys.argv[idx+1:]) + + Logger.static_write(args.log_file, "## Application\nSoftware :" + sys.argv[0] + " (version : " + str(__version__) + ")\nCommand : " + cmd + "\n\n") + html=os.path.abspath(args.html) + data=os.path.abspath(args.data) + matrix=os.path.abspath(args.distance_matrix) + Rscript(html, data, args.varExp, matrix).submit( args.log_file ) diff --git a/tools/phylo_manova/r_manova.xml b/tools/phylo_manova/r_manova.xml new file mode 100755 index 00000000..8fa7f18d --- /dev/null +++ b/tools/phylo_manova/r_manova.xml @@ -0,0 +1,90 @@ + + + + r_manova.py + --data $data + --varExp \"$varExp\" + --distance-matrix $method + --html $html + + + + + + + + + + + + + + + + + + + +.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and `vegan <https://cran.r-project.org/web/packages/vegan/index.html>`_ functions to perform Multivariate Analysis of Variance (MANOVA) + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**data file** (format RData): +The informations of data in one phyloseq object. +This is the result of FROGS Phyloseq Import Data tool. + +**distance file** (format tabular): +The data file containing beta diversity distance matrix. +This file is the result of FROGS Phyloseq Beta Diversity tool. + +.. class:: h3 + +Output + +**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): The review of Manova test. + +.. image:: ${static_path}/images/tools/frogs/phyloseq_manova.png + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@toulouse.inra.fr + +Repository: https://github.com/geraldinepascal/FROGS + +Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf + +Depending on the help provided you can cite us in acknowledgements, references or both. + + + diff --git a/tools/phylo_manova/test.sh b/tools/phylo_manova/test.sh new file mode 100755 index 00000000..fa92fa6a --- /dev/null +++ b/tools/phylo_manova/test.sh @@ -0,0 +1,17 @@ +#!/bin/sh +export PATH=../../libexec:$PATH +export PYTHONPATH=../../lib:$PYTHONPATH + +if [ -d test ] +then + rm -r test/* +else + mkdir test +fi + + +python r_manova.py --data data/data.Rdata \ + --varExp EnvType \ + --distance-matrix data/Unifrac.tsv \ + --html test/phylo_manova.html \ + -l test/phylo_manova.log diff --git a/tools/phylo_structure/.Rhistory b/tools/phylo_structure/.Rhistory new file mode 100644 index 00000000..ba4598c1 --- /dev/null +++ b/tools/phylo_structure/.Rhistory @@ -0,0 +1,42 @@ +library(phyloseq) +source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R") +data <- "data.Rdata" +load(data) +data <- "data/data.Rdata" +load(data) +distance <-"data/Bray_Curtis.tsv" +A <- read.table(file=basename(distance), row.names=1) +A <- read.table(file=distance, row.names=1) +dist <- as.dist(A) +ord <- ordinate(data, method ="MDS", distance = dist) +p1 <- plot_ordination(data, ord, color = "EnvType") + theme_bw() + ggtitle("MDS")+ theme(plot.title = element_text(hjust = 0.5)) +plot(p1) +p2 <- plot_samples(data, ord, color = "EnvType") + theme_bw()+ ggtitle("MDS")+ theme(plot.title = element_text(hjust = 0.5)) +plot(p2) +p22 <- p2 + stat_ellipse(aes(group = EnvType)) +plot(p22) +lowCol <- "#1a9850" # green +midCol <- "#ffffbf" # yellow +highCol <- "#d73027" # red +naCol <- "white" # white! +plot_heatmap(data) + scale_fill_gradient2(low = lowCol, mid = midCol, high = highCol, na.value = naCol, trans = log_trans(4), midpoint = log(100, base = 4))+ facet_grid(~EnvType, scales = "free_x")"+ theme(plot.title = element_text(hjust = 0.5)) + ggtitle("Heatmap plot") +plot(p3) +plot_heatmap(data) +plot_heatmap(data) + scale_fill_gradient2(low = lowCol +) +plot_heatmap(data) + scale_fill_gradient2(low = lowCol, mid = midCol, high = highCol, na.value = naCol, trans = log_trans(4), midpoint = log(100, base = 4)) +plot_heatmap(data) + scale_fill_gradient2(low = lowCol, mid = midCol, high = highCol, na.value = naCol, trans = log_trans(4), midpoint = log(100, base = 4))+ facet_grid(~EnvType, scales = "free_x")+ theme(plot.title = element_text(hjust = 0.5)) + ggtitle("Heatmap plot") +plot(p3) +plot_heatmap(data) + scale_fill_gradient2(low = lowCol, mid = midCol, high = highCol, na.value = naCol, trans = log_trans(4), midpoint = log(100, base = 4))+ facet_grid(~EnvType, scales = "free_x")+ theme(plot.title = element_text(hjust = 0.5)) + ggtitle("Heatmap plot") +plot(p3) +ord <- ordinate(data, method ="MDS", distance = dist) +p1 <- plot_ordination(data, ord, color = "EnvType") + theme_bw() + ggtitle("MDS")+ theme(plot.title = element_text(hjust = 0.5)) +plot(p1) +p2 <- plot_samples(data, ord, color = "EnvType") + theme_bw()+ ggtitle("MDS")+ theme(plot.title = element_text(hjust = 0.5)) +plot(p2) +p22 <- p2 + stat_ellipse(aes(group = EnvType)) +plot(p22) +p3 <- plot_heatmap(data) + scale_fill_gradient2(low = lowCol, mid = midCol, high = highCol, na.value = naCol, trans = log_trans(4), midpoint = log(100, base = 4))+ facet_grid(~EnvType, scales = "free_x") + theme(plot.title = element_text(hjust = 0.5)) + ggtitle("Heatmap plot") +plot(p3) +p3 <- plot_heatmap(data) + scale_fill_gradient2(low = "#ffff00", mid = "#ffa500", high = "#ff0000", na.value = naCol, trans = log_trans(4), midpoint = log(100, base = 4))+ facet_grid(~EnvType, scales = "free_x") + theme(plot.title = element_text(hjust = 0.5)) + ggtitle("Heatmap plot") +plot(p3) diff --git a/tools/phylo_structure/data/Bray_Curtis.tsv 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+ varExp: + value: x + method: + value: x + distance: + value: x +--- + + + + + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` +

FROGS Phyloseq: Structure Visualization

+ + Phyloseq `r packageVersion("phyloseq")` + + +```{r include=FALSE, echo=FALSE} +source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R") +load(params$data) + +#get dist object from distance matrix file +A <- read.table(file=params$distance, row.names=1) +dist <- as.dist(A) +ord <- ordinate(data, method = params$method, distance = dist) +var <- get_variable(data, params$varExp) + +# automatic color palette: one color per different sample type +palette <- hue_pal()(length(levels(var))) +va <- params$varExp +names(palette) <- levels(sample_data(data)$va) + +p1 <- plot_ordination(data, ord, color = params$varExp) + + scale_color_manual(values = palette) + + theme_bw() + ggtitle(paste(params$method,"")) + + theme(plot.title = element_text(hjust = 0.5)) +p2 <- plot_samples(data, ord, color = params$varExp) + + scale_color_manual(values = palette) + theme_bw() + + ggtitle(paste(params$method,"")) + + theme(plot.title = element_text(hjust = 0.5)) +g <- paste('p22 <- p2 + stat_ellipse(aes(group =', params$varExp,'))') +eval(parse(text = g)) + +p3 <- plot_heatmap(data) + scale_fill_gradient2(low = "#ffff00", + mid = "#ffa500", + high = "#ff0000", + na.value = "white", + trans = log_trans(4), + midpoint = log(100, base = 4)) +e <- paste('~', params$varExp) +p3 <- p3 + facet_grid(e, scales = "free_x") + + theme(plot.title = element_text(hjust = 0.5)) + + ggtitle(paste("Heatmap plot with", params$varExp)) +``` + +#{.tabset .tabset-fade .tabset-pills} +##Ordination plot + +

+```{r, fig.width=8, fig.height=6, echo=FALSE, cache=FALSE} +plot(p1) +``` +
+ +

+ +

+```{r, fig.width=8, fig.height=6, echo=FALSE, cache=FALSE} +plot(p2) +``` +
+ +

+ +

+```{r, fig.width=8, fig.height=6, echo=FALSE, cache=FALSE, comment=NA, message=FALSE} +plot(p22) +``` +
+ +

+ + + + + + + +##Heatmap plot +```{r, fig.width=9, fig.height=7, echo=FALSE, cache=FALSE, warning=FALSE} +plot(p3) +``` +
+ + +##R code +

Loading packages & data

+```{r, eval=FALSE} +library(phyloseq) +source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R") +#if you want to generate interactiv plot, load plotly and use ggplotly() instead of plot() +#library(plotly) + +#if in new session +#data <- path to Rdata file containing phyloseq object +#load(data) +#distance <- path to tsv file containing beta diversity distance matrix to use +# A <- read.table(file=distance, row.names=1) +# dist <- as.dist(A) +``` +

Ordianation plots

+```{r, comment=NA, cache=FALSE, echo=FALSE} +cat(paste(sep="","ord <- ordinate(data, method =", '"', params$method,'"', ", distance = dist)")) + +cat(paste(sep="","p1 <- plot_ordination(data, ord, color = ", '"', params$varExp, '"', ") + theme_bw() + ggtitle(", '"', params$method, '")', '+ theme(plot.title = element_text(hjust = 0.5))','\nplot(p1)')) + +cat(paste(sep="","p2 <- plot_samples(data, ord, color = ", '"', params$varExp, '"', ") + theme_bw()+ ggtitle(", '"', params$method, '")', '+ theme(plot.title = element_text(hjust = 0.5))','\nplot(p2)')) + +cat(paste(sep="",'p22 <- p2 + stat_ellipse(aes(group = ', params$varExp,'))', '\nplot(p22)')) +``` + +

Heatmap plot

+```{r, comment=NA, cache=FALSE, echo=FALSE} +cat('# change heatmap color scale with color name or hexadecimal code. see http://tools.medialab.sciences-po.fr/iwanthue/ \nlowCol <- "#ffff00" # yellow\nmidCol <- "#ffa500" # orange\nhighCol <- "#ff0000" # red\nnaCol <- "white" # white!') + +cat(paste(sep="",'p3 <- plot_heatmap(data) + scale_fill_gradient2(low = lowCol, mid = midCol, high = highCol, na.value = naCol, trans = log_trans(4), midpoint = log(100, base = 4))+ facet_grid(~', params$varExp, ', scales = "free_x") + theme(plot.title = element_text(hjust = 0.5)) + ggtitle("Heatmap plot")','\nplot(p3)')) +``` + + + + + + + + + diff --git a/tools/phylo_structure/r_structure.py b/tools/phylo_structure/r_structure.py new file mode 100755 index 00000000..5a7a41c3 --- /dev/null +++ b/tools/phylo_structure/r_structure.py @@ -0,0 +1,100 @@ +#!/usr/bin/env python2.7 +# +# Copyright (C) 2017 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . +# +__author__ = 'Ta Thi Ngan & Maria Bernard INRA - SIGENAE' +__copyright__ = 'Copyright (C) 2017 INRA' +__license__ = 'GNU General Public License' +__version__ = '1.0.0' +__email__ = 'frogs@toulouse.inra.fr' +__status__ = 'prod' + +import os +import sys +import argparse + +CURRENT_DIR = os.path.dirname(os.path.abspath(__file__)) +# PATH +BIN_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "libexec")) +os.environ['PATH'] = BIN_DIR + os.pathsep + os.environ['PATH'] +# PYTHONPATH +LIB_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_DIR), "lib")) +sys.path.append(LIB_DIR) +if os.getenv('PYTHONPATH') is None: os.environ['PYTHONPATH'] = LIB_DIR +else: os.environ['PYTHONPATH'] = os.environ['PYTHONPATH'] + os.pathsep + LIB_DIR + +from frogsUtils import * +################################################################################################################################################## +# +# COMMAND LINES +# +################################################################################################################################################## + +class Rscript(Cmd): + """ + @summary: Launch Rmarkdown script to visualize data structure with phyloseq. + @see: http://rmarkdown.rstudio.com/ + https://joey711.github.io/phyloseq/ + @return: the html file containing the plots. + """ + def __init__(self, html, data, varExp, method, distance): + """ + @params html: [str] Path to store resulting html file containing ordination plot and heatmap plot. + @param data: [str] One phyloseq object in rdata file, the result of FROGS Phyloseq Import Data. + @param varExp: [str] The experiment variable. + @param method: [str] The ordination method,the method in list (MDS, NMDS, DCA, CCA, RDA, CAP, DPCoA). + @param distance: [str] Path of data file containing beta diversity distance matrix. These file is the result of FROGS Phyloseq Beta Diversity. + """ + rmd = os.path.join(CURRENT_DIR, "r_structure.Rmd") + Cmd.__init__( self, + 'Rscript', + 'Run 1 code Rmarkdown', + '-e "rmarkdown::render('+"'"+rmd+"',output_file='"+html+"', params=list(data='"+data+"', varExp='"+varExp+"',method='"+method+"',distance='"+distance+"'), intermediates_dir='"+os.path.dirname(html)+"')"+'" 2> /dev/null', + "-e '(sessionInfo()[[1]][13])[[1]][1]; paste(\"Rmarkdown version: \",packageVersion(\"rmarkdown\")) ; library(phyloseq); paste(\"Phyloseq version: \",packageVersion(\"phyloseq\"))'") + def get_version(self): + """ + @summary: Returns the program version number. + @return: [str] Version number if this is possible, otherwise this method return 'unknown'. + """ + return Cmd.get_version(self, 'stdout') +################################################################################################################################################## +# +# MAIN +# +################################################################################################################################################## + +if __name__ == "__main__": + + # Manage parameters + parser = argparse.ArgumentParser( description='Visulization of data structure with heatmap plot and ordination plot of Phyloseq.') + parser.add_argument('-v', '--varExp', type=str, required=True, default=None, help='The experiment variable you want to analyse.') + parser.add_argument('-m','--method', type=str, default='MDS', choices=["MDS", "NMDS", "DCA", "CCA", "RDA", "CAP", "DPCoA", "PCoA"], help="The ordination methods, the method in list (MDS, NMDS, DCA, CCA, RDA, CAP, DPCoA, PCoA). [Default: %(default)s]") + # Inputs + group_input = parser.add_argument_group( 'Inputs' ) + group_input.add_argument('-d','--data', required=True, default=None, help="The path of RData file containing a phyloseq object-the result of FROGS Phyloseq Import Data" ) + group_input.add_argument('-i','--distance', required=True, default=None, help="Path of data file containing beta diversity distance matrix. These file is the result of FROGS Phyloseq Beta Diversity.") + # output + group_output = parser.add_argument_group( 'Outputs' ) + group_output.add_argument('-o','--html', default='structure.html', help="Path to store resulting html file containing plots. [Default: %(default)s]") + group_output.add_argument( '-l', '--log_file', default=sys.stdout, help='This output file will contain several information on executed commands.') + args = parser.parse_args() + prevent_shell_injections(args) + # Process + Logger.static_write(args.log_file, "## Application\nSoftware :" + sys.argv[0] + " (version : " + str(__version__) + ")\nCommand : " + " ".join(sys.argv) + "\n\n") + html=os.path.abspath(args.html) + data=os.path.abspath(args.data) + distance=os.path.abspath(args.distance) + Rscript(html, data, args.varExp, args.method, distance).submit( args.log_file ) diff --git a/tools/phylo_structure/r_structure.xml b/tools/phylo_structure/r_structure.xml new file mode 100755 index 00000000..6ede83ee --- /dev/null +++ b/tools/phylo_structure/r_structure.xml @@ -0,0 +1,109 @@ + + + + with heatmap plot and ordination plot + r_structure.py + --html $html + --data $data + --varExp $varExp + --method $method + --distance $distance + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. image:: ${static_path}/images/tools/frogs/FROGS_logo.png + :height: 144 + :width: 110 + +.. class:: infomark page-header h2 + +What it does + +Using `phyloseq <https://joey711.github.io/phyloseq/>`_ and customized R function, this tool constructs heatmap plot and ordination plot with the `ordination methods <https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-analysis.html#ordination-methods>`_ to visualise data structure. + +.. class:: infomark page-header h2 + +Inputs/Outputs + +.. class:: h3 + +Input + +**data file** (format rdata): +The informations of data in one phyloseq object. +This file is the result of "FROGS Phyloseq Import Data tool". + +**distance file** (format tabular): +The data file containing beta diversity distance matrix. +This file is the result of "FROGS Phyloseq Beta Diversity tool". + +.. class:: h3 + +Output + +**html file** (format `HTML <https://en.wikipedia.org/wiki/HTML>`_): + +The review of data structure with an ordination plot and with an heatmap plot: + +.. image:: ${static_path}/images/tools/frogs/phyloseq_plot_sample_ellipse.png + :height: 343 + :width: 450 + +.. image:: ${static_path}/images/tools/frogs/phyloseq_plot_heatmap_red.png + :height: 343 + :width: 450 + +.. class:: infomark page-header h2 + +**Contact** + +Contacts: frogs@toulouse.inra.fr + +Repository: https://github.com/geraldinepascal/FROGS + +Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_poster.pdf + +Depending on the help provided you can cite us in acknowledgements, references or both. + + + diff --git a/tools/phylo_structure/test.sh b/tools/phylo_structure/test.sh new file mode 100755 index 00000000..cd88d2d4 --- /dev/null +++ b/tools/phylo_structure/test.sh @@ -0,0 +1,18 @@ +#!/bin/sh +export PATH=../../libexec:$PATH +export PYTHONPATH=../../lib:$PYTHONPATH + +if [ -d test ] +then + rm -r test/* +else + mkdir test +fi + +python r_structure.py \ + --data data/data.Rdata \ + --varExp EnvType \ + --method MDS \ + --distance data/Unifrac.tsv \ + --html test/phylo_structure.html \ + --log_file test/phylo_structure.log diff --git a/tools/tree/tree.xml b/tools/tree/tree.xml index 69127ae6..3bd4b5a0 100755 --- a/tools/tree/tree.xml +++ b/tools/tree/tree.xml @@ -95,7 +95,7 @@ Outputs The phylogenetic tree in Newick format (format `nxh <https://en.wikipedia.org/wiki/Newick_format>`_). - .. image:: ${static_path}/images/tools/frogs/frogs_tree_treefile.png + .. image:: ${static_path}/images/tools/frogs/nwk_treefile.png **Html file** (summary.html):