Mercurial > repos > ppericard > viscorvar
changeset 0:d0b77b926863 draft
"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
| author | ppericard |
|---|---|
| date | Tue, 23 Jun 2020 19:57:35 -0400 |
| parents | |
| children | e93350dc99f1 |
| files | LICENSE README.md additional_functions_block_splsda.R circleCor.xml circleCor_wrapper.R computeMatSimilarity.xml computeMatSimilarity_wrapper.R matCorAddVar.xml matCorAddVar_wrapper.R mixomics_blocksplsda.xml mixomics_blocksplsda_script.R mixomics_plotindiv.xml mixomics_plotindiv_script.R mixomics_plotvar.xml mixomics_plotvar_script.R networkVar.xml networkVar_wrapper.R test-data/in_block1_data.tabular test-data/in_block2_data.tabular test-data/in_sample_meta.tabular test-data/out_plotIndiv.pdf test-data/out_plotVar.pdf test-data/out_rdata.rdata test-data/out_sample_meta.tabular |
| diffstat | 24 files changed, 2319 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,70 @@ +# galaxy-mixomics-blocksplsda +Galaxy wrappers for the block.splsda, plotIndiv and plotVar functions from the mixOmics R package + +# Install for developers + +Clone repository + +``` +$ git clone --recurse-submodules https://gitlab.com/bilille/galaxy-mixomics-blocksplsda.git +``` + +Add `galaxy-mixomics-blocksplsda` repository to `$GALAXYDIR/tools` directory. + +Edit `$GALAXYDIR/config/tool_conf.xml` and add: + +``` +<section id="development" name="Tools development"> + <label id="mixomics_blocksplsda" name="mixOmics blocksplsda" /> + <tool file="galaxy-mixomics-blocksplsda/mixomics_blocksplsda.xml" /> + <tool file="galaxy-mixomics-blocksplsda/mixomics_plotindiv.xml" /> + <tool file="galaxy-mixomics-blocksplsda/mixomics_plotvar.xml" /> + <tool file="galaxy-mixomics-blocksplsda/matCor_addVar.xml" /> + <tool file="galaxy-mixomics-blocksplsda/computeMatSimilarity.xml" /> + <tool file="galaxy-mixomics-blocksplsda/circleCor.xml" /> + <tool file="galaxy-mixomics-blocksplsda/networkVar.xml" /> +</section> +``` + +# Preparing Galaxy conda manual environment for visCorVar + +Activate Galaxy self-installed conda (for your shell; bash here) and reload terminal + +``` +$ . $GALAXYDIR/database/dependencies/_conda/bin/conda init bash +``` + +Create and activate conda environment for visCorVar package + +``` +$ conda create --name __viscorvar@0.1 && conda activate __viscorvar@0.1 +``` + +Install dependencies + +``` +$ conda install bioconductor-mixomics r-rdpack r-igraph +``` + +Manually install visCorVar package from repository + +``` +$ R + +> install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.1.tar.gz", repos=NULL) +> library(visCorVar) +``` + + + + + + + + + + + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/additional_functions_block_splsda.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,104 @@ +#' @title Check if a block contains missing values +#' @description Check if a block contains missing values +#' @param list_X type : list of matrix. This list is used to perform the data integration. +#' @details This function checks if a block contains missing values. +#' @return type : boolean. If at least one block contains missing values, +#' this function returns TRUE, otherwise this function returns FALSE. +#' @examples +#' X1 = matrix(1:9, nrow = 3, ncol = 3) +#' X2 = matrix(10:18, nrow = 3, ncol = 3) +#' list_X = list() +#' list_X[[1]] = X1 +#' list_X[[2]] = X2 +#' names(list_X) = c("X1", "X2") +#' boolean_block_missing_values = blockMissingValues(list_X) +#' @export +blockMissingValues <-function(list_X) +{ + name_blocks = names(list_X) + name_blocks_missing_values = c() + boolean_block_missing_values = FALSE + + for(i in 1:length(list_X)) + { + X_i = list_X[[i]] + name_block_i = name_blocks[i] + + vec = sapply(1:dim(X_i)[2], FUN = function(j){ + res = any(is.na(X_i[, j])) + + return(res) + }) + + if(any(vec)) + { + name_blocks_missing_values = c(name_blocks_missing_values, name_block_i) + + } + + } # End for(i in 1:length(list_X)). + + if(length(name_blocks_missing_values) != 0) + { + stop(paste("The data integration can not be performed if a block contains missing values : ", paste(name_blocks_missing_values, collapse = ", "), " contains missing values. ")) + boolean_block_missing_values = TRUE + + } + + return(boolean_block_missing_values) + +} + + +#' @title Determination of selected variables for all components +#' @description The function unionSelectBlockVariables determines, for each block, the selected block variables +#' for all components. +#' @param res_block_splsda type : sgccda. This parameter is the output of block.splsda function +#' mixOmics. +#' @details For each block, the function unionSelectBlockVariables returns 1 if the block variable is selected for +#' at least one component. Otherwise, this function returns 0. +#' @return type : list of matrix. For each block, if the block variable is selected, the value 1 is associated with +#' this block variable. Otherwise the value 0 is associated with this block variable. +#' @examples +#' data(res_data_integration) +#' list_union_selected_block_variables = unionSelectBlockVariables(res_data_integration) +#' @export +unionSelectBlockVariables <-function(res_block_splsda) +{ + ncomp = res_block_splsda$ncomp[1] + + names_blocks = names(res_block_splsda$loadings) + index_Y = which(names_blocks == "Y") + names_blocks = names_blocks[ - index_Y] + list_select_block_variables = list() + + for(i in 1:length(names_blocks)) + { + mat_loadings_i = res_block_splsda$loadings[[i]] + index_i = c() + + for(j in 1:ncomp) + { + loadings_i_j = mat_loadings_i[, j] + index_i_j = which(loadings_i_j != 0) + + index_i = c(index_i, index_i_j) + + } # End for(j 1:ncomp). + + index_i = unique(index_i) + + mat_select_block_variables = matrix(0, + nrow = dim(mat_loadings_i)[1], + ncol = 1) + mat_select_block_variables[index_i, 1] = rep(1, length(index_i)) + rownames(mat_select_block_variables) = rownames(mat_loadings_i) + + list_select_block_variables[[i]] = mat_select_block_variables + + } # End for(i in 1:length(names_blocks)). + + names(list_select_block_variables) = names_blocks + + return(list_select_block_variables) +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circleCor.xml Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,84 @@ +<tool id="circleCor" name="circleCor" version="1.0" profile="16.04" workflow_compatible="true"> + + <description>plots a correlation circle for the datasets whose correlation circles can be superimposed. This correlation circle contains the selected variables of these datasets which are included in a rectangle and the response variables.</description> + + <requirements> + <requirement type="package" version="6.12">bioconductor-mixomics</requirement> <!-- Remove when viscorvar is available via conda --> + <!-- <requirement type="package" version="0.4">r-ellipse</requirement> --> + <requirement type="package" version="2.0">r-argparse</requirement> + <!-- <requirement type="package" version="1.1">r-rcolorbrewer</requirement> --> + + <!-- <requirement type="package" version="6.8">bioconductor-mixomics</requirement> --> + </requirements> + + <stdio> + <!-- <exit_code range="1:" level="fatal" /> --> + </stdio> + + <command detect_errors="aggressive"> + <![CDATA[ + Rscript + ${__tool_directory__}/circleCor_wrapper.R + --input_rdata ${input_rdata} + --blocks_vec ${select_blocks.value} + --responses_var ${select_responses_var} + --x_min ${x_min} + --x_max ${x_max} + --y_min ${y_min} + --y_max ${y_max} + --output_var ${output_var} + --output_pdf ${output_pdf} + ]]> + </command> + + <inputs> + <param name="input_rdata" type="data" format="rdata" + label="Input RData file" + help="output RData from matCorAddVar"/> + <param name="blocks_vec_list" type="data" format="tabular" + label="List of blocks vector." + help="output *_blocks_comb.tsv file from matCorAddVar"/> + <param name="select_blocks" type="select" + label="Blocks" + help="list of the blocks that are to be superimposed"> + <options from_dataset="blocks_vec_list"> + <column name="value" index="0"/> + <filter type="unique_value" column="0"/> + <filter type="sort_by" name="sorted_value" column="0"/> + </options> + </param> + <param name="responses_var_list" type="data" format="tabular" + label="List of response variables" + help="output *_response_var.tsv file from matCorAddVar"/> + <param name="select_responses_var" type="select" display="checkboxes" + multiple="true" label="Response variables" + help="select the response variables which will be plotted in the correlation circle"> + <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> --> + <options from_dataset="responses_var_list"> + <column name="value" index="0"/> + <filter type="unique_value" column="0"/> + <filter type="sort_by" name="sorted_value" column="0"/> + </options> + </param> + <param name="x_min" type="float" value="-1" min="-1" max="1" + label="X min" help="" /> + <param name="x_max" type="float" value="1" min="-1" max="1" + label="X max" help="" /> + <param name="y_min" type="float" value="-1" min="-1" max="1" + label="Y min" help="" /> + <param name="y_max" type="float" value="1" min="-1" max="1" + label="Y max" help="" /> + </inputs> + + <outputs> + <data name="output_var" format="tabular" label="${tool.name}_selected_var.tsv" /> + <data name="output_pdf" format="pdf" label="${tool.name}.pdf" /> + </outputs> + + <tests> + </tests> + + <help> + </help> + +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circleCor_wrapper.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,131 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Get parameters ## +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Run the circleCor function') + +parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") +parser$add_argument('--blocks_vec', dest='blocks_vec', required=TRUE, help="Blocks vector") +parser$add_argument('--responses_var', dest='responses_var', required=TRUE, help="Responses variables") +parser$add_argument('--x_min', dest='x_min', type='double', required=TRUE, help="X min") +parser$add_argument('--x_max', dest='x_max', type='double', required=TRUE, help="X max") +parser$add_argument('--y_min', dest='y_min', type='double', required=TRUE, help="Y min") +parser$add_argument('--y_max', dest='y_max', type='double', required=TRUE, help="Y max") +parser$add_argument('--output_var', dest='output_var', required=TRUE, help="Output variables file") +parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file") + +args <- parser$parse_args() + +## Print parameters +print("Input RData:") +print(args$input_rdata) +print("Blocks vector:") +print(args$blocks_vec) +print("Response variables:") +print(args$responses_var) +print("X min:") +print(args$x_min) +print("X max:") +print(args$x_max) +print("Y min:") +print(args$y_min) +print("Y max:") +print(args$y_max) +print("Output variables file:") +print(args$output_var) +print("Output PDF file:") +print(args$output_pdf) + +names_blocks = strsplit(args$blocks_vec, ",")[[1]] +names_response_variables = strsplit(args$responses_var, ",")[[1]] + +print("names_blocks:") +print(names_blocks) +print("names_response_variables:") +print(names_response_variables) + +## Loading libraries +# suppressPackageStartupMessages(require(ellipse)) +# suppressPackageStartupMessages(require(grDevices)) +# suppressPackageStartupMessages(require(RColorBrewer)) +# suppressPackageStartupMessages(require(mixOmics)) +## Loading local functions +# source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R") +install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.3.tar.gz", repos=NULL) +suppressPackageStartupMessages(require(visCorVar)) +print("visCorVar has been loaded") + +# R script call +source_local <- function(fname) +{ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} + +# Loading input Rdata file +# loads res_matCorAddVar object +load(args$input_rdata) + +mat_cor_comp1 = res_matCorAddVar$mat_cor_comp1 +mat_cor_comp2 = res_matCorAddVar$mat_cor_comp2 +cutoff_comp = res_matCorAddVar$cutoff_comp +comp = res_matCorAddVar$comp +list_vec_index_block_select = res_matCorAddVar$list_vec_index_block_select +list_vec_names_blocks = res_matCorAddVar$list_vec_names_blocks +list_cor_comp_selected_var_resp_var = res_matCorAddVar$list_cor_comp_selected_var_resp_var +res_compute_cor_var_interest = res_matCorAddVar$res_compute_cor_var_interest +res_block_splsda = res_matCorAddVar$res_block_splsda + +# +print("mat_cor_comp1:") +print(mat_cor_comp1) +print("mat_cor_comp2:") +print(mat_cor_comp2) +print("cutoff_comp:") +print(cutoff_comp) +print("comp:") +print(comp) +print("list_vec_index_block_select:") +print(list_vec_index_block_select) +print("list_vec_names_blocks:") +print(list_vec_names_blocks) +print("list_cor_comp_selected_var_resp_var:") +print(list_cor_comp_selected_var_resp_var) +print("res_compute_cor_var_interest:") +print(res_compute_cor_var_interest) + +# Open output pdf file +pdf(args$output_pdf, width=8, height=7) +mar = c(5, 5, 2, 8) +par(mar = mar) + +selected_variables = circleCor(list_dataframe_cor_comp_var_global = list_cor_comp_selected_var_resp_var, + list_vec_index_block_select = list_vec_index_block_select, + mat_cor_comp1 = mat_cor_comp1, + mat_cor_comp2 = mat_cor_comp2, + names_blocks = names_blocks, + names_response_variables = names_response_variables, + comp = comp, + cutoff = 0.85, + min.X = args$x_min, + max.X = args$x_max, + min.Y = args$y_min, + max.Y = args$y_max, + # vec_col = vec_col, + rad.in = 0.5, + cex = 0.7, + cex_legend = 0.8, + pos = c(1.2, 0), + pch = 20) + +dev.off() + +write(selected_variables, file=args$output_var, ncolumns=1) \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/computeMatSimilarity.xml Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,39 @@ +<tool id="computeMatSimilarity" name="computeMatSimilarity" version="1.0" profile="16.04" workflow_compatible="true"> + + <description>performs the computation of the similarities. The similarity between two variables is an approximation of the correlation between these two variables.</description> + + <requirements> + <requirement type="package" version="6.12">bioconductor-mixomics</requirement> <!-- Remove when viscorvar is available via conda --> + <requirement type="package" version="2.0">r-argparse</requirement> + </requirements> + + <stdio> + <!-- <exit_code range="1:" level="fatal" /> --> + </stdio> + + <command detect_errors="aggressive"> + <![CDATA[ + Rscript + ${__tool_directory__}/computeMatSimilarity_wrapper.R + --input_rdata ${input_rdata} + --output_rdata ${output_rdata} + ]]> + </command> + + <inputs> + <param name="input_rdata" type="data" format="rdata" + label="Input RData file" + help="output RData file from matCorAddVar"/> + </inputs> + + <outputs> + <data name="output_rdata" format="rdata" label="${tool.name}_output.rdata" /> + </outputs> + + <tests> + </tests> + + <help> + </help> + +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/computeMatSimilarity_wrapper.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,53 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Get parameters ## +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Run the computeMatSimilarity function') + +parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") +parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file") + +args <- parser$parse_args() + +## Print parameters +print("Input RData:") +print(args$input_rdata) +print("Output RData:") +print(args$output_rdata) + +## Loading libraries +# suppressPackageStartupMessages(require(mixOmics)) + +# R script call +source_local <- function(fname) +{ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} + +## Loading local functions +# source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R") +install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.3.tar.gz", repos=NULL) +suppressPackageStartupMessages(require(visCorVar)) +print("visCorVar has been loaded") + +# Loading input Rdata file +# loads res_matCorAddVar object +load(args$input_rdata) + +# Run main function +res_compute_mat_similarity = computeMatSimilarity(res_matCorAddVar = res_matCorAddVar) + +liste_mat_similarity_group = res_compute_mat_similarity$liste_mat_similarity_group +res_matCorAddVar = res_compute_mat_similarity$res_matCorAddVar + +save(res_compute_mat_similarity, + file = args$output_rdata) \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matCorAddVar.xml Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,60 @@ +<tool id="matCorAddVar" name="matCorAddVar" version="1.0" profile="16.04" workflow_compatible="true"> + + <description>determine the correlation circles that can be overlaid and compute the correlations</description> + + <requirements> + <requirement type="package" version="6.12">bioconductor-mixomics</requirement> <!-- Remove when viscorvar is available via conda --> + <requirement type="package" version="2.0">r-argparse</requirement> + <!-- <requirement type="package" version="0.3">viscorvar</requirement> --> + </requirements> + + <stdio> + <!-- <exit_code range="1:" level="fatal" /> --> + </stdio> + + <command detect_errors="aggressive"> + <![CDATA[ + Rscript + ${__tool_directory__}/matCorAddVar_wrapper.R + --input_rdata ${input_rdata} + ##--cutoff_comp ${cutoff_comp} + --cutoff_comp 0.775 + #if str($var_of_interest_file) !='': + --interest_var_file ${var_of_interest_file} + #end if + --block_Y_file ${block_Y} + --output_rdata ${output_rdata} + --output_response_var ${output_response_var} + --output_blocks_comb ${output_blocks_comb} + ]]> + </command> + + <inputs> + <param name="input_rdata" type="data" format="rdata" + label="Input RData file from block.SPLSDA" + help="This is the RData output file from the block.splsda function." /> + <param name="block_Y" type="data" format="tabular" + label="Block Y" + help="[block_Y] (tabular format) This table contains the name of the samples in the first column. The other columns correspond to phenotypes. For each of these other columns, a column determines which sample is associated with this phenotype (value equals to 1) or not (value equals to 0). The name of the samples in Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order" /> + <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur --> + <param name="var_of_interest_file" type="data" format="txt" optional="true" + label="Variables of interest (Optional)" + help="these variables have to belong to datasets that can be superimposed"/> +<!-- <param name="cutoff_comp" type="float" value="0.775" min="0" max="1" + label="Cutoff comp" + help="[cutoff_comp] Two correlation circles will be superimposed if the correlation of their first and second axis is greater than cutoff_comp in absolute value." /> --> + </inputs> + + <outputs> + <data name="output_rdata" format="rdata" label="${tool.name}_output.rdata" /> + <data name="output_response_var" format="tabular" label="${tool.name}_response_var.tsv" /> + <data name="output_blocks_comb" format="tabular" label="${tool.name}_blocks_comb.tsv" /> + </outputs> + + <tests> + </tests> + + <help> + </help> + +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matCorAddVar_wrapper.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,115 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Get parameters ## +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Compute the matCorEtBlockSelect and addVariablesReponses functions') + +parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") +parser$add_argument('--cutoff_comp', dest='cutoff_comp', type='double', required=TRUE, help="") +parser$add_argument('--interest_var_file', dest='interest_var_file', required=FALSE, help="Variables of interest file") +parser$add_argument('--block_Y_file', dest='block_Y_file', required=TRUE, help="Block Y filepath") +parser$add_argument('--output_rdata', dest='output_rdata', required=TRUE, help="Output RData file") +parser$add_argument('--output_response_var', dest='output_response_var', required=TRUE, help="Output response variables file") +parser$add_argument('--output_blocks_comb', dest='output_blocks_comb', required=TRUE, help="Output blocks combinations file") + +args <- parser$parse_args() + +## Print parameters +print("Input RData:") +print(args$input_rdata) +print("Cutoff comp:") +print(args$cutoff_comp) +print("Variables of interest:") +print(args$interest_var_file) +print("Block Y file:") +print(args$block_Y_file) +print("Output RData:") +print(args$output_rdata) +print("Output Response variables:") +print(args$output_response_var) +print("Output Blocks combinations:") +print(args$output_blocks_comb) + +## Loading libraries +# source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R") +install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.3.tar.gz", repos=NULL) +suppressPackageStartupMessages(require(visCorVar)) +print("visCorVar has been loaded") + +# R script call +source_local <- function(fname) +{ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} + +# Loading input Rdata file +load(args$input_rdata) + +ncomp = mixomics_result$ncomp + +# Reading Block Y matrix +print("Reading Block Y") +mat_block_Y = read.table(args$block_Y_file, header=TRUE, row.names=1) +print(mat_block_Y) + +response_var = colnames(mat_block_Y) + +print("response_var:") +print(response_var) + +# Write response variables to output file +invisible(lapply(response_var, write, file=args$output_response_var, append=TRUE, ncolumns=1)) + +# Reading var of intereset file +interest_var_vec = NULL +if (args$interest_var_file != 'None') { + interest_var_vec = as.character(read.table(args$interest_var_file, header=FALSE)[[1]]) +} + +# +comp = 1:2 + +# Running main function +res_matCorAddVar = matCorAddVar(res_block_splsda = mixomics_result, + block_Y = mat_block_Y, + cutoff_comp = args$cutoff_comp, + var_interest = interest_var_vec, + comp = comp) + +# +mat_cor_comp1 = res_matCorAddVar$mat_cor_comp1 +mat_cor_comp2 = res_matCorAddVar$mat_cor_comp2 +list_vec_index_block_select = res_matCorAddVar$list_vec_index_block_select +list_vec_names_blocks = res_matCorAddVar$list_vec_names_blocks +list_cor_comp_selected_var_resp_var = res_matCorAddVar$list_cor_comp_selected_var_resp_var +res_compute_cor_var_interest = res_matCorAddVar$res_compute_cor_var_interest + +# +print("mat_cor_comp1:") +print(mat_cor_comp1) +print("mat_cor_comp2:") +print(mat_cor_comp2) +print("list_vec_index_block_select:") +print(list_vec_index_block_select) +print("list_vec_names_blocks:") +print(list_vec_names_blocks) +print("list_cor_comp_selected_var_resp_var:") +print(list_cor_comp_selected_var_resp_var) +print("res_compute_cor_var_interest:") +print(res_compute_cor_var_interest) + +# Write all possible blocks combinations to output file +invisible(lapply(list_vec_names_blocks, write, file=args$output_blocks_comb, append=TRUE, ncolumns=100, sep=",")) + +# Save all objects in Rdata output file +save(res_matCorAddVar, + file = args$output_rdata)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_blocksplsda.xml Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,268 @@ +<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="1.0" profile="16.04" workflow_compatible="true"> + + <description>performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis</description> + + <requirements> + <requirement type="package" version="6.12">bioconductor-mixomics</requirement> + <requirement type="package" version="2.0">r-argparse</requirement> + </requirements> + +<!-- <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> --> + + <command detect_errors="aggressive"> + <![CDATA[ + mkdir outdir + && Rscript + ${__tool_directory__}/mixomics_blocksplsda_script.R + #for $b in $blocks + --block + #if $b.block_name + ${b.block_name} + #else + ${b.data_matrix.name} + #end if + ${b.keep} + ${b.data_matrix} + ${b.variable_metadata} + #end for + --sample_metadata_in ${sample_metadata_in} + --sample_description_col ${sample_description_col} + --ncomp ${adv.ncomp} + ${correlation} + ##--scheme ${adv.scheme} + ##--mode ${adv.mode} + --maxiter ${adv.maxiter} + ##${adv.scale} + --scale ## always activated hidden param + ${adv.check_missing_values} + ##--init ${adv.init} + ##--tol ${adv.tol} + ##${adv.nearzerovar} + --rdata_out ${rdata_out} + --sample_metadata_out ${sample_metadata_out} + --variable_metadata_outdir outdir + ]]> + </command> + + <inputs> + <repeat name="blocks" title="Blocks"> + <param name="block_name" type="text" label="Block name" /> + <param name="keep" type="integer" value="0" min="0" + label="Number of variables to select for each component" + help="[keep] Estimation of the number of variables in the block correlated with variables from the other blocks and correlated with response variables. If set to 0, all variables will be selected." /> + <param name="data_matrix" type="data" format="tabular" + label="Data matrix" + help="Block data in tabular format (rows = variables, columns = samples). The first column contains the variables names and the first row contains the samples names. Samples names must be in the same order for all blocks and the sample metadata (transposed). The data must not contain missing values." /> + <param name="variable_metadata" type="data" format="tabular" optional="true" + label="Variables metadata [optional]" + help="Variables metadata in tabular format (rows = variables). The first colum contains the variables names. The first row contains the metadata column names. The number of rows in the metadata file must be the same than the number of rows in the block data file, and the variables need to be in the same order. If a metadata file is provided, block.splsda output will be appended as new columns, otherwise a new file will be created." /> + </repeat> + <param name="sample_metadata_in" type="data" format="tabular" + label="Samples metadata" + help="Samples metadata in tabular format (rows = samples). The first column contains the sample names. The first row contains the metadata column names. Samples names must be in the same order (transposed) than all the blocks. One of the column (the last by default) must contain the samples groups for integration." /> + <param name="sample_description_col" type="integer" value="0" min="0" + label="Samples groups column number" + help="Column from the samples metadata file containing samples groups. If set to 0, the last column will be used." /> + <param name="correlation" type="boolean" truevalue="--correlation" + falsevalue="" checked="false" + label="Correlation between all blocks" + help="[design] If set to Yes, data integration will take into account correlations between all the blocks (design matrix with diagonal coefficients set to 0 and the rest of the coefficients set to 1)." /> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="ncomp" type="integer" value="2" min="1" + label="Number of components to include in the model" + help="[ncomp] Number of new variables (components) computed by the data integration." /> +<!-- <param name="scheme" type="select" label="Scheme"> + <option value="horst" selected="true">horst</option> + <option value="factorial" >factorial</option> + <option value="centroid" >centroid</option> + </param> + <param name="mode" type="select" label="Mode"> + <option value="regression" selected="true">regression</option> + <option value="canonical" >canonical</option> + <option value="invariant" >invariant</option> + <option value="classic" >classic</option> + </param> --> + <param name="maxiter" type="integer" value="100" min="1" + label="Maximum number of iterations" + help="[max.iter] Maximum number of iterations performed by block.splsda." /> +<!-- <param name="scale" type="boolean" truevalue="-\-scale" falsevalue="" checked="true" + label="Scale" + help="if checked, each block is standardized to zero means and unit variances" /> --> + <param name="check_missing_values" type="boolean" truevalue="-\-check_missing_values" falsevalue="" checked="true" + label="Check for missing values" + help="will raise an error if missing values are found in data matrices" /> +<!-- <param name="init" type="select" label="Init"> + <option value="svd" selected="true">svd</option> + <option value="svd.single" >svd.single</option> + </param> + <param name="tol" type="float" value="1e-06" min="0" + label="Convergence stopping value" + help="[tol]" /> + <param name="nearzerovar" type="boolean" truevalue="-\-nearzerovar" falsevalue="" checked="true" + label="Should be set to TRUE in particular for data with many zero values" /> --> + </section> + </inputs> + + <outputs> + <data name="rdata_out" format="rdata" label="${tool.name}_output.rdata" /> + <data name="sample_metadata_out" format="tabular" + label="${tool.name}_${sample_metadata_in.name}" /> + <collection name="blocks_output" type="list" label="${tool.name}_blocks_output"> + <discover_datasets pattern="(?P<designation>.+)\.tsv" + directory="outdir" format="tabular" /> + </collection> + </outputs> + + <tests> + <test> + <repeat name="blocks"> + <param name="block_name" value="Block1" /> + <param name="data_matrix" value="in_block1_data.tabular" /> + </repeat> + <repeat name="blocks"> + <param name="block_name" value="Block2" /> + <param name="data_matrix" value="in_block2_data.tabular" /> + </repeat> + <param name="sample_metadata_in" value="in_sample_meta.tabular" /> + <output name="rdata_out" value="out_rdata.rdata" /> + <output name="sample_metadata_out" value="out_sample_meta.tabular" /> + </test> + </tests> + + <help> + <![CDATA[ +.. class:: infomark + +**Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr) + +--------------------------------------------------- + +.. class:: infomark + +**Please cite** + +Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration. +PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752 + +--------------------------------------------------- + +====================== +mixOmics blocks.splsda +====================== + +----------- +Description +----------- + +The blocks.splsda function is part of the mixOmics package for exploration and integration of Omics datasets. +Performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis. + +----------- +Input files +----------- + +For each block (min 2 blocks): +============================== + ++------------------------------+------------+ +| Parameter : num + label | Format | ++==============================+============+ +| 1 : Data matrix | tabular | ++------------------------------+------------+ +| 2 : [opt] Variables metadata | tabular | ++------------------------------+------------+ + +Variables metadata files are optional. +If a file is provided, output metadata will be appended to the input file, otherwise a new output file will be created. + +1. Data matrix format + * Rows = variables, Columns = samples + * First row = samples name. MUST be the same and in the same order in every block as well as in the sample metadata file (transposed) + * First column = variables name + +2. Variables metadata format + * Rows = variables, Columns = metadata + * First row = metadata column names + * First column = variables names. MUST be the same and in the same order than in the associated data matrix + +Global input files: +=================== + ++-----------------------------+------------+ +| Parameter : num + label | Format | ++=============================+============+ +| 1 : Samples metadata | tabular | ++-----------------------------+------------+ + +By default, the last column of the samples metadata matrix will be used as samples description factors. +If it's not the case, the column number can be inputed in the `Sample description column number` parameter. + +1. Samples metadata format + * Rows = samples, Columns = metadata + * First row = metadata column names + * First column = sample names. These names must be identical (transposed) and in the same order than for the blocks data matrices + +---------- +Parameters +---------- + +For each block (min 2 blocks): +============================== + +Block name + Name of the block. If not provided, this will default to the input filename + +Number of variables to select for each component + If set to 0 (default), all variables will be considered in the model + +Global parameters: +================== + +Sample description column number + +Number of components to include in the model + +Correlation between all blocks + +Advanced options: +================= + +Scheme + +Mode + +Maximum number of iterations + +Scale + +Init + +Convergence stopping value (tol) + +Near zero var + +------------ +Output files +------------ + +mixomics_blocksplsda_output.rdata + | rData output + | Contains the `mixomics_result` R object containing the result of the block.splsda function + +mixomics_blocksplsda_{input_sample_metadata_name} + | tabular output + | Identical to the input Sample metadata file with appended columns from the result of block.splsda function + +mixomics_blocksplsda_blocks_output + A collection with the variable metadata output files (mixomics_blocksplsda_block_{block name}_variable_metadata) for each input block + + ]]> + </help> + + <citations> + <citation type="doi">10.1371/journal.pcbi.1005752</citation> + </citations> + +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_blocksplsda_script.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,233 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Get parameters ## +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Run the mixOmics block.splsda function') + +parser$add_argument('--block', dest='blocks_list', nargs=4, action="append", required=TRUE, + help="Block name + nb variables to select + data matrix file + variables metadata file") +parser$add_argument('--sample_metadata_in', dest='sample_metadata_in', required=TRUE, + help="Samples metadata file") +parser$add_argument('--sample_description_col', dest='sample_description_col', type='integer', + default=0, help="Sample description column number") +parser$add_argument('--ncomp', dest='ncomp', type='integer', default=2, + help="Number of components to include in the model") +parser$add_argument('--correlation', dest='correlation', action="store_true", + help="Add correlation between all blocks") +parser$add_argument('--scheme', dest='scheme', default="horst", help="Scheme") +parser$add_argument('--mode', dest='mode', default="regression", help="Mode") +parser$add_argument('--maxiter', dest='maxiter', type='integer', default=100, + help="Maximum number of iterations") +parser$add_argument('--scale', dest='scale', action="store_true", + help="Each block is standardized to zero means and unit variances") +parser$add_argument('--check_missing_values', dest='check_missing_values', action="store_true", + help="Check for missing values and raise an error") +parser$add_argument('--init', dest='init', default="svd", + help="Init (svd or svd.single)") +parser$add_argument('--tol', dest='tol', type='double', default=1e-06, + help="Convergence stopping value") +parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true", + help="Should be set in particular for data with many zero values") +parser$add_argument('--rdata_out', dest='rdata_out', required=TRUE, help="Output Rdata file") +parser$add_argument('--sample_metadata_out', dest='sample_metadata_out', required=TRUE, help="Output sample metadata file") +parser$add_argument('--variable_metadata_outdir', dest='variable_metadata_outdir', required=TRUE, help="Output variable metadata directory") + +args <- parser$parse_args() + +## Print parameters +print("Blocks:") +print(args$blocks_list) +print("Sample metadata file:") +print(args$sample_metadata_in) +print("Sample description column number:") +print(args$sample_description_col) +print("Number of components:") +print(args$ncomp) +print("Compute correlation between all blocks:") +print(args$correlation) +print("Scheme:") +print(args$scheme) +print("Mode:") +print(args$mode) +print("Max nb of iterations:") +print(args$maxiter) +print("Scale:") +print(args$scale) +print("Check for missing values:") +print(args$check_missing_values) +print("Tol:") +print(args$tol) +print("near.zero.var:") +print(args$nearzerovar) +print("Output Rdata file:") +print(args$rdata_out) +print("Output sample metadata file:") +print(args$sample_metadata_out) +print("Output variable metadata directory:") +print(args$variable_metadata_outdir) + +## Loading libraries +suppressPackageStartupMessages(require(mixOmics)) + +## Read sample metadata file and set description factor matrix +sample_metadata <- read.table(args$sample_metadata_in, sep='\t', header=TRUE, row.names=1) +sample_metadata_names <- row.names(sample_metadata) +# print(sample_metadata_names) + +# print("Sample metadata matrix:") +# print(head(sample_metadata)) + +description_column <- ncol(sample_metadata) +if(args$sample_description_col > 0) +{ + description_column <- args$sample_description_col +} + +Y <- factor(sample_metadata[[description_column]]) + +print("Y factor matrix:") +print(Y) + +## Read and prepare block datasets +list_X <- c() +keepX <- c() + +for(i in 1:nrow(args$blocks_list)) +{ + # Read block input parameters + block_name <- args$blocks_list[i,1] + block_keep <- strtoi(args$blocks_list[i,2]) + block_data_matrix_filename <- args$blocks_list[i,3] + # block_meta_var <- args$blocks_list[i,4] + + print(sprintf("Processing block %s", block_name)) + + # Store block data matrices + block_data_matrix <- t(read.table(block_data_matrix_filename, sep='\t', header=TRUE, row.names=1)) # transpose the matrix so that the samples become rows and the variables become columns + block_data_matrix_names <- row.names(block_data_matrix) + # print(block_data_matrix_names) + + if(!identical(sample_metadata_names, block_data_matrix_names)) + { + stop("Sample names must be the same and in the same order in the sample metadata matrix and the block data matrix") + } + + list_X[[block_name]] <- block_data_matrix + + # Set the nb of variables to keep + nb_variables = ncol(list_X[[block_name]]) + if(block_keep > 0) + { + keepX[[block_name]] <- rep(block_keep, args$ncomp) + } + else + { + keepX[[block_name]] <- rep(nb_variables, args$ncomp) + } + print(sprintf("Block %s contains %d variables and %d will be selected", block_name, nb_variables, block_keep)) +} + +# print(list_X) + +## Generate design matrix +block_nb <- nrow(args$blocks_list) + +design <- matrix(0, nrow = block_nb, ncol = block_nb) + +if(args$correlation) +{ + design <- matrix(1, nrow = block_nb, ncol = block_nb) + diag(design) <- 0 +} + +# print("Design matrix:") +# print(design) + +################### +## Main function ## +################### + +mixomics_result <- block.splsda(X = list_X, + Y = Y, + ncomp = args$ncomp, + keepX = keepX, + design = design, + scheme = args$scheme, + mode = args$mode, + scale = args$scale, + init = args$init, + tol = args$tol, + max.iter = args$maxiter, + near.zero.var = args$nearzerovar, + all.outputs = TRUE) + +print("Block.splsda object:") +print(mixomics_result) +print(attributes(mixomics_result)) + +## Save output Rdata file +save(mixomics_result, file=args$rdata_out) + +## Save output sample metadata file +# print("Block.splsda variates:") +# print(mixomics_result$variates) + +for(block_name in names(mixomics_result$variates)) +{ + # print(block_name) + # print(mixomics_result$variates[[block_name]]) + + # Format the column names to add the block name and replace spaces + colnames(mixomics_result$variates[[block_name]]) <- paste("block.splsda_variates", block_name, gsub(" ", "_", colnames(mixomics_result$variates[[block_name]])), sep = "_") + # print(mixomics_result$variates[[block_name]]) + + # Append the new columns to the sample metadata matrix + sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[block_name]]) +} + +# print(sample_metadata) + +write.table(sample_metadata, file = args$sample_metadata_out, quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA) + +## Save output variable metadata files in output directory +# print("Block.splsda loadings:") +# print(mixomics_result$loadings) + +for(i in 1:nrow(args$blocks_list)) +{ + # Read again block input parameters + block_name <- args$blocks_list[i,1] + # block_keep <- strtoi(args$blocks_list[i,2]) + # block_data_matrix_filename <- args$blocks_list[i,3] + block_meta_var <- args$blocks_list[i,4] + + print(sprintf("Saving block %s output metavar", block_name)) + + meta_variable <- mixomics_result$loadings[[block_name]] + # print(head(meta_variable)) + + # Format the column names to add the block name and replace spaces + colnames(meta_variable) <- paste("block.splsda_loadings", gsub(" ", "_", colnames(meta_variable)), sep = "_") + + # Read input block variable metadata files if provided (optional) + if(block_meta_var != "None") + { + input_meta_variable <- read.table(block_meta_var, sep='\t', header=TRUE, row.names=1) + # print(head(input_meta_variable)) + + # Append the new columns to the variable metadata matrix + meta_variable <- cbind2(input_meta_variable, meta_variable) + } + + # print(head(meta_variable)) + + block_meta_var_output_filename <- paste("mixomics_blocksplsda_block_", block_name, "_variable_metadata.tsv", sep="") + write.table(meta_variable, file = paste(args$variable_metadata_outdir,block_meta_var_output_filename, sep='/'), quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA) +} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_plotindiv.xml Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,111 @@ +<tool id="mixomics_plotindiv" name="mixOmics plotIndiv" version="1.0" profile="16.04" workflow_compatible="true"> + + <description>provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA)</description> + + <requirements> + <requirement type="package" version="6.12">bioconductor-mixomics</requirement> + <requirement type="package" version="2.0">r-argparse</requirement> + </requirements> + + <stdio> + <!-- <exit_code range="1:" level="fatal" /> --> + </stdio> + + <command detect_errors="aggressive"> + <![CDATA[ + Rscript + ${__tool_directory__}/mixomics_plotindiv_script.R + --input_rdata $input_rdata + $adv.legend + $adv.ellipse + --output_pdf $output_pdf + ]]> + </command> + + <inputs> + <param name="input_rdata" type="data" format="rdata" + label="Input RData file from (sparse)(I)PCA, (regularized)CCA, (sparse)PLS(DA) or (sparse)(R)GCCA(DA)" + help="This is the RData output file from the block.splsda function." /> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="legend" type="boolean" checked="true" truevalue="--legend" falsevalue="" + label="Plot legend" /> + <param name="ellipse" type="boolean" checked="true" truevalue="--ellipse" falsevalue="" + label="Plot ellipse plots" /> + </section> + </inputs> + + <outputs> + <data name="output_pdf" format="pdf" label="plotIndiv.pdf" /> + </outputs> + + <tests> + <test> + <param name="input_rdata" value="out_rdata.rdata" /> + <output name="output_pdf" value="out_plotIndiv.pdf" /> + </test> + </tests> + + <help> + <![CDATA[ +.. class:: infomark + +**Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr) + +--------------------------------------------------- + +.. class:: infomark + +**Please cite** + +Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration. +PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752 + +--------------------------------------------------- + +================== +mixOmics plotIndiv +================== + +----------- +Description +----------- + +The plotIndiv function is part of the mixOmics package for exploration and integration of Omics datasets. +Provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA). + +----------- +Input files +----------- + ++-------------------------------+------------+ +| Parameter : num + label | Format | ++===============================+============+ +| 1 : Rdata block.splsda output | Rdata | ++-------------------------------+------------+ + +---------- +Parameters +---------- + +Advanced options: +================= + +Plot legend + +Plot ellipse plots + +------------ +Output files +------------ + +plotIndiv.pdf + A pdf file with scatter plots for individuals + + ]]> + </help> + + <citations> + <citation type="doi">10.1371/journal.pcbi.1005752</citation> + </citations> + +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_plotindiv_script.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,53 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Get parameters ## +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Run the mixOmics plotIndiv function') + +parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") +parser$add_argument('--legend', dest='legend', action="store_true", help="Display the legend") +parser$add_argument('--ellipse', dest='ellipse', action="store_true", help="Plot ellipse plots") +parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file") + +args <- parser$parse_args() + +## Print parameters +print("Input RData:") +print(args$input_rdata) +print("Plot legend:") +print(args$legend) +print("Plot ellipse plots:") +print(args$ellipse) +print("Output PDF file:") +print(args$output_pdf) + +# loading libraries +suppressPackageStartupMessages(require(mixOmics)) + +load(args$input_rdata) + +pdf(args$output_pdf) + +# plotIndiv(mixomics_result, +# legend = args$legend, +# ellipse = args$ellipse) + +for(k in 1:(length(mixomics_result$names[[3]])-1)) +{ + name_block = mixomics_result$names[[3]][k] + + try(plotIndiv(mixomics_result, + blocks = k, + legend = args$legend, + ellipse = args$ellipse), + silent = FALSE) +} + +dev.off() \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_plotvar.xml Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,112 @@ +<tool id="mixomics_plotvar" name="mixOmics plotVar" version="1.0" profile="16.04" workflow_compatible="true"> + + <description>provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA</description> + + <requirements> + <requirement type="package" version="6.12">bioconductor-mixomics</requirement> + <requirement type="package" version="2.0">r-argparse</requirement> + </requirements> + + <stdio> + <!-- <exit_code range="1:" level="fatal" /> --> + </stdio> + + <command detect_errors="aggressive"> + <![CDATA[ + Rscript + ${__tool_directory__}/mixomics_plotvar_script.R + --input_rdata $input_rdata + $adv.legend + --cutoff $adv.cutoff + --output_pdf $output_pdf + ]]> + </command> + + <inputs> + <param name="input_rdata" type="data" format="rdata" + label="Input RData file from (sparse)(I)PCA, (regularized)CCA, (sparse)PLS(DA) or (sparse)(R)GCCA(DA)" + help="This is the RData output file from the block.splsda function." /> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="legend" type="boolean" checked="true" truevalue="--legend" falsevalue="" + label="Plot legend" /> + <param name="cutoff" type="float" value="0" min="0" max="1" + label="Cut-off" + help="Only selected variables whose correlation with the first or second axis is greater than Cut-off in absolute value will be plotted." /> + </section> + </inputs> + + <outputs> + <data name="output_pdf" format="pdf" label="plotVar.pdf" /> + </outputs> + + <tests> + <test> + <param name="input_rdata" value="out_rdata.rdata" /> + <output name="output_pdf" value="out_plotVar.pdf" /> + </test> + </tests> + + <help> + <![CDATA[ +.. class:: infomark + +**Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr) + +--------------------------------------------------- + +.. class:: infomark + +**Please cite** + +Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration. +PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752 + +--------------------------------------------------- + +================ +mixOmics plotVar +================ + +----------- +Description +----------- + +The plotVar function is part of the mixOmics package for exploration and integration of Omics datasets. +Provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA. + +----------- +Input files +----------- + ++-------------------------------+------------+ +| Parameter : num + label | Format | ++===============================+============+ +| 1 : Rdata block.splsda output | Rdata | ++-------------------------------+------------+ + +---------- +Parameters +---------- + +Advanced options: +================= + +Plot legend + +Cut-off + +------------ +Output files +------------ + +plotIndiv.pdf + A pdf file with scatter plots for individuals + + ]]> + </help> + + <citations> + <citation type="doi">10.1371/journal.pcbi.1005752</citation> + </citations> + +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixomics_plotvar_script.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,56 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Main Function ## + +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Run the mixOmics plotVar function') + +parser$add_argument('--input_rdata', dest='input_rdata', required=TRUE, help="Input RData file") +parser$add_argument('--legend', dest='legend', action="store_true", help="Display the legend") +parser$add_argument('--cutoff', dest='cutoff', type='double', required=TRUE, help="Cutoff (0..1)") +parser$add_argument('--output_pdf', dest='output_pdf', required=TRUE, help="Output PDF file") + +args <- parser$parse_args() + +## +print("Input RData:") +print(args$input_rdata) +print("Plot legend:") +print(args$legend) +print("Cutoff:") +print(args$cutoff) +print("Output PDF file:") +print(args$output_pdf) + +# loading libraries +suppressPackageStartupMessages(require(mixOmics)) + +load(args$input_rdata) + +pdf(args$output_pdf) + +# plotVar(mixomics_result, +# legend = args$legend, +# cutoff = args$cutoff) + +for(k in 1:(length(mixomics_result$names[[3]])-1)) +{ + name_block = mixomics_result$names[[3]][k] + + # We're still continuing even if a graph is empty + try(plotVar(mixomics_result, + blocks = k, + legend = args$legend, + cutoff = args$cutoff), + silent = FALSE) + +} + +dev.off() \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/networkVar.xml Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,64 @@ +<tool id="networkVar" name="networkVar" version="1.0" profile="16.04" workflow_compatible="true"> + + <description>creates a network between selected variables of datasets and the response variables. In the network, the similarity between two variables is associated with the link between these two variables.</description> + + <requirements> + <requirement type="package" version="6.12">bioconductor-mixomics</requirement> <!-- Remove when viscorvar is available via conda --> + <requirement type="package" version="1.2">r-igraph</requirement> + <requirement type="package" version="2.0">r-argparse</requirement> + </requirements> + + <stdio> + <!-- <exit_code range="1:" level="fatal" /> --> + </stdio> + + <command detect_errors="aggressive"> + <![CDATA[ + Rscript + ${__tool_directory__}/networkVar_wrapper.R + --mat_similarity_rdata ${mat_similarity_rdata} + --var_list_file ${var_list_file} + --response_var ${select_response_var} + --output_graph ${output_graph} + ]]> + </command> + + <inputs> + <param name="mat_similarity_rdata" type="data" format="rdata" + label="Input computeMatSimilarity RData file" + help="output RData file from computeMatSimilarity"/> + <param name="var_list_file" type="data" format="tabular" + label="Variables list file" + help="selected variables output tabular file from circleCor"/> + + <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur --> + <!-- <param name="var_of_interest_file" type="data" format="txt" optional="true" + label="Variables of interest (Optional)" + help="these variables have to belong to datasets that can be superimposed"/> --> + + <param name="response_var_list" type="data" format="tabular" + label="List of response variables" + help="output *_response_var.tsv file from matCorAddVar"/> + <param name="select_response_var" type="select" display="checkboxes" multiple="true" + label="Response variables" + help="response variables that will be plotted in the network"> + <!-- <param name="select_responses_var" type="select" multiple="true" label="Response variables"> --> + <options from_dataset="response_var_list"> + <column name="value" index="0"/> + <filter type="unique_value" column="0"/> + <filter type="sort_by" name="sorted_value" column="0"/> + </options> + </param> + </inputs> + + <outputs> + <data name="output_graph" format="xml" label="${tool.name}_graph.graphml" /> + </outputs> + + <tests> + </tests> + + <help> + </help> + +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/networkVar_wrapper.R Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,81 @@ +#!/usr/bin/env Rscript + +# Setup R error handling to go to stderr +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Get parameters ## +suppressPackageStartupMessages(require(argparse)) + +parser <- ArgumentParser(description='Run the networkVar function') + +parser$add_argument('--mat_similarity_rdata', dest='mat_similarity_rdata', required=TRUE, help="matSimilarity RData file") +parser$add_argument('--var_list_file', dest='var_list_file', required=TRUE, help="Variables list file") +# parser$add_argument('--interest_var_file', dest='interest_var_file', required=FALSE, help="Variables of interest file") +parser$add_argument('--response_var', dest='response_var', required=TRUE, help="Response variables") +parser$add_argument('--output_graph', dest='output_graph', required=TRUE, help="Output graphml") + +args <- parser$parse_args() + +## Print parameters +print("matSimilarity RData file:") +print(args$mat_similarity_rdata) +print("Variables list file:") +print(args$var_list_file) +# print("Variables of interest:") +# print(args$interest_var_file) +print("Response variables:") +print(args$response_var) +print("Output graphml:") +print(args$output_graph) + +## Loading libraries +# suppressPackageStartupMessages(require(mixOmics)) +suppressPackageStartupMessages(require(igraph)) + +# R script call +source_local <- function(fname) +{ + argv <- commandArgs(trailingOnly = FALSE) + base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) + source(paste(base_dir, fname, sep="/")) +} + +## Loading local functions +# source_local("mixomics-blocksplsda-integration/integration_block_splsda_func.R") +install.packages("https://gitlab.com/bilille/mixomics-blocksplsda-integration/-/raw/master/visCorVar_0.3.tar.gz", repos=NULL) +suppressPackageStartupMessages(require(visCorVar)) +print("visCorVar has been loaded") + +# Loading input Rdata file +# loads res_compute_mat_similarity object +load(args$mat_similarity_rdata) + +# +names_block_variables = as.character(read.table(args$var_list_file, header=FALSE)[[1]]) +names_response_variables = strsplit(args$response_var, ",")[[1]] + +# interest_var_vec = NULL +# if (args$interest_var_file != 'None') { +# interest_var_vec = as.character(read.table(args$interest_var_file, header=FALSE)[[1]]) +# } + +print("names_block_variables:") +print(names_block_variables) +# print("interest_var_vec:") +# print(interest_var_vec) +print("names_response_variables:") +print(names_response_variables) + +res_networkVar = networkVar(res_compute_mat_similarity = res_compute_mat_similarity, + names_block_variables = names_block_variables, + names_response_variables = names_response_variables, + cutoff = 0) + +print("networkVar() completed") +print("res_networkVar:") +print(res_networkVar) + +write.graph(res_networkVar$gR, file = args$output_graph, format = "graphml") \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_block1_data.tabular Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,7 @@ + "A1" "A2" "B1" "B2" +"var1" 1 2 3 4 +"var2" 1.5 2.5 3.5 4.5 +"var3" 2.5 2 2.5 2 +"var4" 5 4 3 2 +"var5" 1.001 1.01 1.1 1 +"var6" 10 13 11 10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_block2_data.tabular Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,7 @@ + "A1" "A2" "B1" "B2" +"var1" 2 3 4 5 +"var2" 2.5 1 2.5 4 +"var3" 2.5 2 2.5 2 +"var4" 6 5 3 2 +"var5" 10.001 10.01 10.1 10 +"var6" 20 23 21 20
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_sample_meta.tabular Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,5 @@ + "Y" +"A1" "catA" +"A2" "catA" +"B1" "catB" +"B2" "catB"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_sample_meta.tabular Tue Jun 23 19:57:35 2020 -0400 @@ -0,0 +1,5 @@ +"" "Y" "block.splsda_Block1_comp1" "block.splsda_Block1_comp2" "block.splsda_Block2_comp1" "block.splsda_Block2_comp2" "block.splsda_Y_comp1" "block.splsda_Y_comp2" +"A1" "catA" 1.85013467343542 0.422684485040581 1.28016568038406 0.405956759170116 1.22474487139159 0.0342790721507239 +"A2" "catA" 1.07324868851916 -0.960001503242697 1.53872954309497 -0.749531756995324 1.22474487139159 -0.16259622770647 +"B1" "catB" -1.0856729590951 1.64317643604658 -1.01949098398762 1.60513370686125 -1.22474487139159 0.374128476201717 +"B2" "catB" -1.83771040285949 -1.10585941784446 -1.79940423949142 -1.26155870903602 -1.22474487139159 -0.245811320645977