To install the matrixBP package, you can use the following command in R:
devtools::install_github('IDSS-NIAID/matrixBP')
library(matrixBP)Loading required package: deeptime
Loading required package: ggplot2
Loading required package: patchwork
library(dplyr)Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
library(RColorBrewer)
library(cowplot)Attaching package: 'cowplot'
The following object is masked from 'package:patchwork':
align_plots
theme_set(theme_cowplot())
# Load the data
data(metlip)
# colors for facet_grid labels
grp_colors <- levels(metlip$Group) |>
length() |>
brewer.pal('Set3')
names(grp_colors) <- levels(metlip$Group)
# plot with colored facets
matrix_barplot(metlip, aes(x = Lipid, y = neg_log_p, color = log2FC),
cols = vars(Group), rows = vars(sample), facet_colors = grp_colors) |>
mBP_legend()Warning: Removed 11 rows containing missing values or values outside the scale range
(`geom_rect()`).
# plot in portrait orientation
matrix_barplot(metlip, aes(x = neg_log_p, y = Lipid, color = log2FC),
cols = vars(sample), rows = vars(Group), facet_colors = grp_colors,
orientation = 'portrait') |>
mBP_legend()Warning: Removed 11 rows containing missing values or values outside the scale range
(`geom_rect()`).
# change the color of the bars
g1 <- matrix_barplot(metlip, aes(x = Lipid, y = neg_log_p, color = log2FC),
cols = vars(Group), rows = vars(sample), facet_colors = grp_colors) +
scale_color_gradient2(low = 'purple3', high = 'orange3')Scale for colour is already present.
Adding another scale for colour, which will replace the existing scale.
mBP_legend(g1)Warning: Removed 11 rows containing missing values or values outside the scale range
(`geom_rect()`).
# plots with labeled facets
matrix_barplot(metlip, aes(x = Lipid, y = neg_log_p, color = log2FC),
cols = vars(Acyl_1), rows = vars(sample)) |>
mBP_col_labels()
matrix_barplot(metlip, aes(x = neg_log_p, y = Lipid, color = log2FC),
cols = vars(sample), rows = vars(Group), facet_colors = grp_colors,
orientation = 'portrait') |>
mBP_row_labels()
# plot with 12 samples
(g <- metlip |>
bind_rows(mutate(metlip, sample = paste0(sample, 1)),
mutate(metlip, sample = paste0(sample, 2))) |>
matrix_barplot(aes(x = Lipid, y = neg_log_p, color = log2FC),
cols = vars(Group), rows = vars(sample), facet_colors = grp_colors) |>
mBP_legend())Warning: Removed 11 rows containing missing values or values outside the scale range
(`geom_rect()`).
# larger plots seem to have trouble rendering in RStudio, but saving them as a file works
#ggsave('12_samples.png', g, width = 10, height = 10)
# trying to plot multiple samples on a single row causes the colors not to work
# add a catch that will notify the user if they try to do this
matrix_barplot(metlip, aes(x = Lipid, y = neg_log_p, color = log2FC),
cols = vars(Group), facet_colors = grp_colors) |>
mBP_legend()Warning: The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
Warning: The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
The following aesthetics were dropped during statistical transformation:
colour.
ℹ This can happen when ggplot fails to infer the correct grouping structure in
the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
variable into a factor?
Warning: Removed 11 rows containing missing values or values outside the scale range
(`geom_rect()`).
# try adding `na.rm = TRUE` to `scale_...` to see if that gets rid of warnings about NA values