annotate mixomics_blocksplsda.R @ 2:c8533e9298e5 draft

"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"

#!/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")
    }

    if(any(is.na(block_data_matrix)))
    {
        stop(sprintf("Block %s contains missing values. We recommend not to perform data integration with missing values. If you want to force run, change the advanced parameter 'Check for missing values' to 'No'.", block_name))
    }

    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)

# 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="/"))
}

# Load library
source_local("mixomics_blocksplsda_additional_funct.R")


list_union_selected_block_variables = unionSelectBlockVariables(mixomics_result)

## 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 <- list_union_selected_block_variables[[i]]
    colnames(meta_variable) <- "block.splsda_var_select"

    # 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)
}