-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
✨ test if adding packages one by one works
- should also fail faster as installations are done first - add msImpute again
- Loading branch information
enryh
committed
Dec 27, 2024
1 parent
43b9d1b
commit e9e56c4
Showing
4 changed files
with
413 additions
and
3 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,176 @@ | ||
| # --- | ||
| # jupyter: | ||
| # jupytext: | ||
| # formats: ipynb,R:light | ||
| # text_representation: | ||
| # extension: .R | ||
| # format_name: light | ||
| # format_version: '1.5' | ||
| # jupytext_version: 1.14.5 | ||
| # kernelspec: | ||
| # display_name: R | ||
| # language: R | ||
| # name: ir | ||
| # --- | ||
|
|
||
| # + tags=["parameters"] vscode={"languageId": "r"} | ||
| methods = 'KNN_IMPUTE,msImpute' | ||
|
|
||
| # + tags=["hide-input"] vscode={"languageId": "r"} | ||
| # options("install.lock"=FALSE) | ||
|
|
||
| packages_base_R <- | ||
| c("BiocManager", "reshape2", "data.table", "readr", "tibble") | ||
|
|
||
| install_rpackage <- function(pkg) { | ||
| # If not installed, install the package | ||
| if (!require(pkg, character.only = TRUE)) { | ||
| install.packages(pkg) | ||
| library(pkg, character.only = TRUE) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| # used in the large imputation function for two packages | ||
| install_bioconductor <- function(pkg) { | ||
| # If not installed, install the package | ||
| if (!require(pkg, character.only = TRUE)) { | ||
| BiocManager::install(pkg) | ||
| library(pkg, character.only = TRUE) | ||
| } | ||
|
|
||
| } | ||
|
|
||
|
|
||
| nafunctions <- function(method = "zero") { | ||
| method <- tolower(method) | ||
| if (method == "zero") { | ||
| } | ||
| else if (method == "minimum") { | ||
| } | ||
| else if (method == "colmedian") { | ||
| install_rpackage('e1071') | ||
| } | ||
| else if (method == "rowmedian") { | ||
| install_rpackage('e1071') | ||
| } | ||
| else if (method == "knn_impute") { | ||
| install_bioconductor('impute') | ||
| } | ||
| else if (method == "seqknn") { | ||
| if (!require(SeqKnn)) { | ||
| install.packages("src/R_NAGuideR/SeqKnn_1.0.1.tar.gz", | ||
| repos = NULL, | ||
| type = "source") | ||
| } | ||
| } | ||
| else if (method == "bpca") { | ||
| install_bioconductor('pcaMethods') | ||
| } | ||
| else if (method == "svdmethod") { | ||
| install_bioconductor('pcaMethods') | ||
| } | ||
| else if (method == "lls") { | ||
| install_bioconductor('pcaMethods') | ||
| } | ||
| else if (method == "mle") { | ||
| install_rpackage('norm') | ||
| } | ||
| else if (method == "qrilc") { | ||
| install_bioconductor("impute") | ||
| install_bioconductor("pcaMethods") | ||
| install_rpackage('gmm') | ||
| install_rpackage('imputeLCMD') | ||
| } | ||
| else if (method == "mindet") { | ||
| install_bioconductor("impute") | ||
| install_bioconductor("pcaMethods") | ||
| install_rpackage('gmm') | ||
| install_rpackage('imputeLCMD') | ||
| } | ||
| else if (method == "minprob") { | ||
| install_bioconductor("impute") | ||
| install_bioconductor("pcaMethods") | ||
| install_rpackage('gmm') | ||
| install_rpackage('imputeLCMD') | ||
| } | ||
| else if (method == "irm") { | ||
| install_rpackage('VIM') | ||
| } | ||
| else if (method == "impseq") { | ||
| install_rpackage('rrcovNA') | ||
| } | ||
| else if (method == "impseqrob") { | ||
| install_rpackage('rrcovNA') | ||
| } | ||
| else if (method == "mice-norm") { | ||
| install_rpackage('mice') | ||
| } | ||
| else if (method == "mice-cart") { | ||
| install_rpackage('mice') | ||
| } | ||
| else if (method == "trknn") { | ||
| source('src/R_NAGuideR/Imput_funcs.r') | ||
| } | ||
| else if (method == "rf") { | ||
| install_rpackage("missForest") | ||
| } | ||
| else if (method == "pi") { | ||
| } | ||
| # else if(method=="grr"){ | ||
| # library(DreamAI) | ||
| # df<-impute.RegImpute(data=as.matrix(df1), fillmethod = "row_mean", maxiter_RegImpute = 10,conv_nrmse = 1e-03) | ||
| # } | ||
| else if (method == "gms") { | ||
| # install.packages('GMSimpute') | ||
| if (!require(GMSimpute)) { | ||
| install.packages( | ||
| "src/R_NAGuideR/GMSimpute_0.0.1.1.tar.gz", | ||
| repos = NULL, | ||
| type = "source" | ||
| ) | ||
| } | ||
| } | ||
| else if (method == "msimpute") { | ||
| install_bioconductor("msImpute") | ||
| } | ||
| else if (method == "msimpute_mnar") { | ||
| install_bioconductor("msImpute") | ||
| } | ||
| else if (method == "gsimp") { | ||
| options(stringsAsFactors = F) | ||
| # dependencies parly for sourced file | ||
|
|
||
| install_bioconductor("impute") | ||
| install_bioconductor("pcaMethods") | ||
| install_rpackage('gmm') | ||
| install_rpackage('imputeLCMD') | ||
| install_rpackage("magrittr") | ||
| install_rpackage("glmnet") | ||
| install_rpackage("abind") | ||
| install_rpackage("foreach") | ||
| install_rpackage("doParallel") | ||
| source('src/R_NAGuideR/GSimp.R') | ||
|
|
||
| } | ||
| else{ | ||
| stop(paste("Unspported methods so far: ", method)) | ||
| } | ||
| df <- as.data.frame(df) | ||
| df | ||
| } | ||
|
|
||
|
|
||
| for (package in packages_base_R) { | ||
| # Check if the package is already installed | ||
| install_rpackage(pkg = package) | ||
| } | ||
|
|
||
|
|
||
| # + vscode={"languageId": "r"} | ||
| methods = unlist(strsplit(methods, split = ",")) | ||
| for (package in methods) { | ||
| # Check if the package is already installed, otherwise install | ||
| nafunctions(method = package) | ||
| } | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,219 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "e470a0a5", | ||
| "metadata": { | ||
| "tags": [ | ||
| "parameters" | ||
| ], | ||
| "vscode": { | ||
| "languageId": "r" | ||
| } | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "methods = 'KNN_IMPUTE,msImpute'" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "7ffb0a1b", | ||
| "metadata": { | ||
| "lines_to_next_cell": 2, | ||
| "tags": [ | ||
| "hide-input" | ||
| ], | ||
| "vscode": { | ||
| "languageId": "r" | ||
| } | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# options(\"install.lock\"=FALSE)\n", | ||
| "\n", | ||
| "packages_base_R <-\n", | ||
| " c(\"BiocManager\", \"reshape2\", \"data.table\", \"readr\", \"tibble\")\n", | ||
| "\n", | ||
| "install_rpackage <- function(pkg) {\n", | ||
| " # If not installed, install the package\n", | ||
| " if (!require(pkg, character.only = TRUE)) {\n", | ||
| " install.packages(pkg)\n", | ||
| " library(pkg, character.only = TRUE)\n", | ||
| " }\n", | ||
| " \n", | ||
| "}\n", | ||
| "\n", | ||
| "# used in the large imputation function for two packages\n", | ||
| "install_bioconductor <- function(pkg) {\n", | ||
| " # If not installed, install the package\n", | ||
| " if (!require(pkg, character.only = TRUE)) {\n", | ||
| " BiocManager::install(pkg)\n", | ||
| " library(pkg, character.only = TRUE)\n", | ||
| " }\n", | ||
| " \n", | ||
| "}\n", | ||
| "\n", | ||
| "\n", | ||
| "nafunctions <- function(method = \"zero\") {\n", | ||
| " method <- tolower(method)\n", | ||
| " if (method == \"zero\") {\n", | ||
| " }\n", | ||
| " else if (method == \"minimum\") {\n", | ||
| " }\n", | ||
| " else if (method == \"colmedian\") {\n", | ||
| " install_rpackage('e1071')\n", | ||
| " }\n", | ||
| " else if (method == \"rowmedian\") {\n", | ||
| " install_rpackage('e1071')\n", | ||
| " }\n", | ||
| " else if (method == \"knn_impute\") {\n", | ||
| " install_bioconductor('impute')\n", | ||
| " }\n", | ||
| " else if (method == \"seqknn\") {\n", | ||
| " if (!require(SeqKnn)) {\n", | ||
| " install.packages(\"src/R_NAGuideR/SeqKnn_1.0.1.tar.gz\",\n", | ||
| " repos = NULL,\n", | ||
| " type = \"source\")\n", | ||
| " }\n", | ||
| " }\n", | ||
| " else if (method == \"bpca\") {\n", | ||
| " install_bioconductor('pcaMethods')\n", | ||
| " }\n", | ||
| " else if (method == \"svdmethod\") {\n", | ||
| " install_bioconductor('pcaMethods')\n", | ||
| " }\n", | ||
| " else if (method == \"lls\") {\n", | ||
| " install_bioconductor('pcaMethods')\n", | ||
| " }\n", | ||
| " else if (method == \"mle\") {\n", | ||
| " install_rpackage('norm')\n", | ||
| " }\n", | ||
| " else if (method == \"qrilc\") {\n", | ||
| " install_bioconductor(\"impute\")\n", | ||
| " install_bioconductor(\"pcaMethods\")\n", | ||
| " install_rpackage('gmm')\n", | ||
| " install_rpackage('imputeLCMD')\n", | ||
| " }\n", | ||
| " else if (method == \"mindet\") {\n", | ||
| " install_bioconductor(\"impute\")\n", | ||
| " install_bioconductor(\"pcaMethods\")\n", | ||
| " install_rpackage('gmm')\n", | ||
| " install_rpackage('imputeLCMD')\n", | ||
| " }\n", | ||
| " else if (method == \"minprob\") {\n", | ||
| " install_bioconductor(\"impute\")\n", | ||
| " install_bioconductor(\"pcaMethods\")\n", | ||
| " install_rpackage('gmm')\n", | ||
| " install_rpackage('imputeLCMD')\n", | ||
| " }\n", | ||
| " else if (method == \"irm\") {\n", | ||
| " install_rpackage('VIM')\n", | ||
| " }\n", | ||
| " else if (method == \"impseq\") {\n", | ||
| " install_rpackage('rrcovNA')\n", | ||
| " }\n", | ||
| " else if (method == \"impseqrob\") {\n", | ||
| " install_rpackage('rrcovNA')\n", | ||
| " }\n", | ||
| " else if (method == \"mice-norm\") {\n", | ||
| " install_rpackage('mice')\n", | ||
| " }\n", | ||
| " else if (method == \"mice-cart\") {\n", | ||
| " install_rpackage('mice')\n", | ||
| " }\n", | ||
| " else if (method == \"trknn\") {\n", | ||
| " source('src/R_NAGuideR/Imput_funcs.r')\n", | ||
| " }\n", | ||
| " else if (method == \"rf\") {\n", | ||
| " install_rpackage(\"missForest\")\n", | ||
| " }\n", | ||
| " else if (method == \"pi\") {\n", | ||
| " }\n", | ||
| " # else if(method==\"grr\"){\n", | ||
| " # library(DreamAI)\n", | ||
| " # df<-impute.RegImpute(data=as.matrix(df1), fillmethod = \"row_mean\", maxiter_RegImpute = 10,conv_nrmse = 1e-03)\n", | ||
| " # }\n", | ||
| " else if (method == \"gms\") {\n", | ||
| " # install.packages('GMSimpute')\n", | ||
| " if (!require(GMSimpute)) {\n", | ||
| " install.packages(\n", | ||
| " \"src/R_NAGuideR/GMSimpute_0.0.1.1.tar.gz\",\n", | ||
| " repos = NULL,\n", | ||
| " type = \"source\"\n", | ||
| " )\n", | ||
| " }\n", | ||
| " }\n", | ||
| " else if (method == \"msimpute\") {\n", | ||
| " install_bioconductor(\"msImpute\")\n", | ||
| " }\n", | ||
| " else if (method == \"msimpute_mnar\") {\n", | ||
| " install_bioconductor(\"msImpute\")\n", | ||
| " }\n", | ||
| " else if (method == \"gsimp\") {\n", | ||
| " options(stringsAsFactors = F)\n", | ||
| " # dependencies parly for sourced file\n", | ||
| " \n", | ||
| " install_bioconductor(\"impute\")\n", | ||
| " install_bioconductor(\"pcaMethods\")\n", | ||
| " install_rpackage('gmm')\n", | ||
| " install_rpackage('imputeLCMD')\n", | ||
| " install_rpackage(\"magrittr\")\n", | ||
| " install_rpackage(\"glmnet\")\n", | ||
| " install_rpackage(\"abind\")\n", | ||
| " install_rpackage(\"foreach\")\n", | ||
| " install_rpackage(\"doParallel\")\n", | ||
| " source('src/R_NAGuideR/GSimp.R')\n", | ||
| " \n", | ||
| " } \n", | ||
| " else{\n", | ||
| " stop(paste(\"Unspported methods so far: \", method))\n", | ||
| " }\n", | ||
| " df <- as.data.frame(df)\n", | ||
| " df\n", | ||
| "}\n", | ||
| "\n", | ||
| "\n", | ||
| "for (package in packages_base_R) {\n", | ||
| " # Check if the package is already installed\n", | ||
| " install_rpackage(pkg = package)\n", | ||
| "}" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "1d65b5d9", | ||
| "metadata": { | ||
| "vscode": { | ||
| "languageId": "r" | ||
| } | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "methods = unlist(strsplit(methods, split = \",\"))\n", | ||
| "for (package in methods) {\n", | ||
| " # Check if the package is already installed, otherwise install\n", | ||
| " nafunctions(method = package)\n", | ||
| "}\n" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "jupytext": { | ||
| "formats": "ipynb,R:light" | ||
| }, | ||
| "kernelspec": { | ||
| "display_name": "R", | ||
| "language": "R", | ||
| "name": "ir" | ||
| }, | ||
| "language_info": { | ||
| "name": "R" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } |
Oops, something went wrong.