plot_pca.xml

<!--# 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>