Mercurial > repos > artbio > gsc_center_scale
changeset 0:bcbd7179d8ec draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
| author | artbio |
|---|---|
| date | Thu, 11 Jul 2019 13:31:20 -0400 |
| parents | |
| children | a96cc346819c |
| files | center_scale.R center_scale.xml test-data/full_center.tab test-data/full_standardize.tab test-data/group_center.tab test-data/group_standardize.tab test-data/mini.data.counts.tsv test-data/mini.data.factor.tsv |
| diffstat | 8 files changed, 427 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/center_scale.R Thu Jul 11 13:31:20 2019 -0400 @@ -0,0 +1,101 @@ +options( show.error.messages=F, + error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") +warnings() +library(optparse) + +# Arguments +option_list = list( + make_option( + '--data', + default = NA, + type = 'character', + help = "Input file that contains values to transform. Must be tabular separated, + with columns and row names, variables in rows, observations in columns [default : '%default' ]" + ), + make_option( + '--center', + default = TRUE, + type = 'logical', + help = "center data to the mean [default : '%default' ]" + ), + make_option( + '--scale', + default = TRUE, + type = 'logical', + help = "scale data to standard deviation [default : '%default' ]" + ), + make_option( + '--factor', + default = '', + type = 'character', + help = "A two-column observations|factor_levels table, to group observations to be transformed by levels [default : '%default' ]" + ), + make_option( + '--output', + default = 'res.tab', + type = 'character', + help = "Table of transformed values [default : '%default' ]" + ) +) + +transform <- function(df, center=TRUE, scale=TRUE) { + transfo <- scale( + t(df), + center=center, + scale=center + ) + return(as.data.frame(t(transfo))) +} + +opt = parse_args(OptionParser(option_list = option_list), + args = commandArgs(trailingOnly = TRUE)) + +data = read.table( + opt$data, + check.names = FALSE, + header = TRUE, + row.names = 1, + sep = '\t' +) + +if (opt$factor != '') { + data.factor = read.table( + opt$factor, + check.names = FALSE, + header = TRUE, + sep = '\t' + ) + colnames(data.factor) <- c("cellid", "level") + data.transformed <- data.frame(row.names=rownames(data), stringsAsFactors=FALSE) + for (group in levels(data.factor$level)){ + subcells <- as.data.frame(subset(data.factor, level==group, select=cellid)) + subdata <- as.data.frame(subset(data, select=subcells$cellid)) + subdata.transformed <- transform(subdata, center=opt$center, scale=opt$scale) + data.transformed <- cbind(data.transformed, subdata.transformed) + } +} else { + data.transformed <- transform(data, center=opt$center, scale=opt$scale) +} + + +write.table( + cbind(gene=rownames(data.transformed), data.transformed), + opt$output, + col.names = TRUE, + row.names = FALSE, + quote = F, + sep = "\t" +) + + + + + + + + + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/center_scale.xml Thu Jul 11 13:31:20 2019 -0400 @@ -0,0 +1,105 @@ +<tool id="center_scale" name="Center or scale (standardize) data" version="0.9.0"> + <description></description> + <requirements> + <requirement type="package" version="1.6.0">r-optparse</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Tool exception" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + Rscript $__tool_directory__/center_scale.R + --data '$input' + --center '$center' + --scale '$scale' + #if $factor.factor_options == 'TRUE': + --factor '$file' + #end if + --output '$output' +]]></command> + <inputs> + <param name="input" type="data" format="tabular" label="Input file with values to transform" + help="Must be tabular separated with columns and row names, variables in rows, observations in columns" /> + <param name="center" type="select" label="Center data to mean"> + <option value="TRUE" selected="true">Yes</option> + <option value="FALSE">No</option> + </param> + <param name="scale" type="select" label="Scale data to standard deviation"> + <option value="TRUE" selected="true">Yes</option> + <option value="FALSE">No</option> + </param> + <conditional name="factor"> + <param name="factor_options" type="select" label="group data by factor ?"> + <option value="TRUE">Yes</option> + <option value="FALSE" selected="true">No</option> + </param> + <when value="TRUE"> + <param name="file" type="data" format="tabular" label="Grouping map" + help="A two-column observation|factor_level table that assigns group ids to observations" /> + </when> + <when value="FALSE"> + </when> + </conditional> + </inputs> + <outputs> + <data name="output" format="tabular" label="scale ${on_string}" /> + </outputs> + <tests> + <test> + <param name="input" value="mini.data.counts.tsv" ftype="tabular"/> + <output name="output" file="full_standardize.tab" ftype="tabular"/> + </test> + <test> + <param name="input" value="mini.data.counts.tsv" ftype="tabular"/> + <param name="scale" value="FALSE"/> + <output name="output" file="full_center.tab" ftype="tabular"/> + </test> + <test> + <param name="input" value="mini.data.counts.tsv" ftype="tabular" /> + <param name="factor_options" value="TRUE" /> + <param name="file" value="mini.data.factor.tsv" ftype="tabular" /> + <output name="output" file="group_standardize.tab" ftype="tabular"/> + </test> + <test> + <param name="input" value="mini.data.counts.tsv" ftype="tabular" /> + <param name="scale" value="FALSE"/> + <param name="factor_options" value="TRUE" /> + <param name="file" value="mini.data.factor.tsv" ftype="tabular" /> + <output name="output" file="group_center.tab" ftype="tabular"/> + </test> + </tests> + <help> + +**What it does** + +The tool perform various normalization operations on a data table, including mean centering, +standard deviation rescaling, or both (standardization). + +In addition, these operations can be performed on subsets of observations, is the user provides +a two-column table that maps observations to groups (factor levels). + +**Inputs** + +A data table with observations (samples, library sequencings) in columns (library names +are column names) and variables (genes) in rows (gene names are row names). + +Optionally, a two-column table may be used to map observations to a factor level. In this +case, normalization operations will be performed by group having same level. + +**Outputs** + +A table with same numbers of columns and rows as input table, and transformed values. + + </help> + <citations> + <citation type="bibtex"> + @Manual{, + title = {R: A Language and Environment for Statistical Computing}, + author = {{R Core Team}}, + organization = {R Foundation for Statistical Computing}, + address = {Vienna, Austria}, + year = {2014}, + url = {http://www.R-project.org/}, + } + </citation> + </citations> +</tool>
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