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| author | vmarcon |
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| date | Mon, 23 Oct 2017 09:34:56 -0400 |
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<!--# Copyright (C) 2017 INRA # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see http://www.gnu.org/licenses/. #--> <tool id="plot_pca" name="Plot PCA" version="1.0.0"> <description>PCA analysis</description> <requirements> <requirement type="package">R</requirement> <requirement type="package">r-optparse</requirement> <requirement type="package">r-reshape</requirement> <requirement type="package">r-ggplot2</requirement> <requirement type="package">r-gridextra</requirement> <requirement type="package">r-scatterplot3d</requirement> </requirements> <stdio> <!-- Anything other than zero is an error --> <exit_code range="1:" level="fatal"/> <exit_code range=":-1" level="fatal"/> </stdio> <command><![CDATA[ Rscript $__tool_directory__/plot_pca.R --input_matrix $input_matrix #if $log_cond.log10: -l $log_cond.pseudocount #end if #if $height --height $height #end if #if $width --width $width #end if #if $output --output $output #end if #if $metadata_cond.metadata: --metadata $metadata_cond.input_metadata #for $i, $s in enumerate( $metadata_cond.series ) ,${s.input_metadata2} #end for #if $metadata_cond.color_by --color_by $metadata_cond.color_by #end if #if $metadata_cond.shape_by --shape_by $metadata_cond.shape_by #end if #end if --border --palette=$__tool_directory__/rainbow.3.txt && cp *.pdf $outputfile ]]></command> <inputs> <param argument="--input_matrix" type="data" format="csv,tabular" label="Input Matrix"/> <conditional name="log_cond"> <param name="log10" type="boolean" checked="false" truevalue="True" falsevalue="" label="Apply the log10" help="Default=No"/> <when value="True"> <param name="pseudocount" type="float" value="1e-04" help="Default=1e-04" /> </when> </conditional> <conditional name="metadata_cond"> <param name="metadata" type="boolean" checked="false" truevalue="Yes" falsevalue="" label="Add file with metadata on matrix experiment?" help="must countain a key column named 'labExpId"/> <when value="Yes"> <param name="input_metadata" type="data" format="tsv" label="Input Metadata file"/> <repeat name="series" title="Others Input Metadata files"> <param name="input_metadata2" type="data" format="tsv" label="Other Input Metadata file"/> </repeat> <param argument="--color_by" type="text" label="Choose the fields in the metadata you want to color by" /> <param argument="--shape_by" type="text" label="Choose the fields in the metadata you want to shape by" /> </when> </conditional> <param argument="--height" size="20" type="integer" value="7" label="Height of the plot in inches" /> <param argument="--width" size="20" type="integer" value="7" label="Width of the plot in inches" /> <param argument="--output" type="text" label="Output name" help="[Optional] Specify the project label for your outputs. By default it will be the name of your input file."/> </inputs> <outputs> <data format="pdf" name="outputfile" label ="#if str($output)=='' then os.path.splitext(str($input_matrix.name))[0] else $output #_PCA.pdf"/> </outputs> <tests> <test> <param name="input_matrix" value="decathlon.tsv" /> <conditional name="log_cond"> <param name="log10" value="True" /> <param name="pseudocount" value="1e-04" /> </conditional> <conditional name="metadata_cond"> <param name="metadata" value="" /> </conditional> <param name="height" value="7" /> <param name="width" value="7" /> <param name="output" value="" /> <output name="outputfile" file="output" compare="sim_size" /> </test> </tests> <help><![CDATA[ ======== Plot PCA ======== ----------- Description ----------- Plot a Principal Component Analysis (PCA) from a data matrix ----------- Input files ----------- +---------------------------+----------------+ | Parameter : num + label | Format | +===========================+================+ | 1 : Input matrix | csv,tabular | +---------------------------+----------------+ ---------- Parameters ---------- Apply the log 10 | To normalize your data | (?)Add file with metadata on matrix experiment? | To ad metadata to the analysis | Input Metadata file | Must countain a key column named labExpId | Others Metadata files | Choose the fields in the metadata you want to color by | Choose the fields in the metadata you want to shape by | Height of the plot in inches | default 7 inches | Width of the plot in inches | default 7 inches | Output name | Specify the project label for your outputs. By default it will be the name of your input file | ------------ Output files ------------ <Input Name>_PCA.pdf | Pdf file containing your PCA plot ------ **Authors** Alessandra Breschi (alessandra.breschi@crg.eu); Sarah Djebali (sarah.djebali-quelen@inra.fr); Valentin Marcon (valentin.marcon@inra.fr) Contact : sigenae-support@listes.inra.fr ------------- Please cite : ------------- - (Depending on the help provided you can cite us in acknowledgements) Acknowledgements | We wish to thank : Alessandra Breschi, Sarah Djebali (Centre for Genomic Regulation - http://www.crg.eu/), and Valentin Marcon (Migale platform - http://migale.jouy.inra.fr/) ------ .. class:: infomark Usage: ./plot_pca.R [options] file Options: -i INPUT_MATRIX, --input_matrix=INPUT_MATRIX the matrix you want to analyze. Can be stdin -l, --log10 apply the log [default=FALSE] -p PSEUDOCOUNT, --pseudocount=PSEUDOCOUNT specify a pseudocount for the log [default=1e-04] -m METADATA, --metadata=METADATA A list of tsv files with metadata on matrix experiment. They must be in the format 'file1.tsv,file2.tsv' and contain a key column named 'labExpId'. Can be omitted --merge_mdata_on=MERGE_MDATA_ON [default=labExpId] -c COLOR_BY, --color_by=COLOR_BY choose the fields in the metadata you want to color by --sort_color=SORT_COLOR A field for sorting colors. Can be omitted [default=NULL] -s SHAPE_BY, --shape_by=SHAPE_BY choose the fields in the metadata you want to shape by --no_legend Do not show the legend [default=FALSE] -r, --row_as_variables select this if you want rows as variables [default=FALSE] -C PRINCOMP, --princomp=PRINCOMP choose the principal components you want to plot. With 3 PC it gives a 3d plot [default='PC1,PC2'] --print_scores Output the resuling PCs as a separate file with the extension PCs.tsv [default=FALSE] --print_loadings Output the resulting loadings as a separate file with the extension loadings.tsv [default=FALSE] --print_lambdas Output the resulting lambdas (stdev) as a separate file with the extension lambdas.tsv [default=FALSE] --biplot If active, the factor of the color is used as grouping factor. Centroids are computed and the first <top> loadings are plotted wrt to the two specified components [default=FALSE] --palette=PALETTE File with the color palette [default=/users/rg/abreschi/R/palettes/cbbPalette1.15.txt] --border Black border to dots [default=FALSE] --shapes=SHAPES File with the shapes [default=NULL] -L LABELS, --labels=LABELS The metadata field with the labels [default=NULL] -B BASE_SIZE, --base_size=BASE_SIZE Base font size [default=16] -H HEIGHT, --height=HEIGHT Height of the plot in inches [default=7] -W WIDTH, --width=WIDTH Width of the plot in inches [default=7] -o OUTPUT, --output=OUTPUT output file name [default=pca.out] -v, --verbose verbose output [default=FALSE] -h, --help Show this help message and exit ]]></help> </tool>