Mercurial > repos > lecorguille > pca
changeset 0:79c7fdc90ed6 draft default tip
Uploaded
| author | lecorguille |
|---|---|
| date | Tue, 30 Jun 2015 06:38:09 -0400 |
| parents | |
| children | |
| files | abims_acp.r abims_acp.xml static/images/anova_filtered.png static/images/anova_pvalue.png static/images/hclust.png static/images/pca_abims_Rplots.png static/images/pca_abims_Rplots1.png static/images/pca_abims_eigenvalue.png static/images/pca_abims_percentage_of_variance.png |
| diffstat | 9 files changed, 217 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_acp.r Tue Jun 30 06:38:09 2015 -0400 @@ -0,0 +1,46 @@ +#!/usr/local/public/bin/Rscript +# abims_acp.r version="1.1" + +# date: 04-06-2013 +# **Authors** Gildas Le Corguille ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr + + + +#function PCA from package FactoMineR + +library(batch) +library(FactoMineR) + +acp_metabolomics=function(file ,graph=FALSE, scale.unit=TRUE, sep=";", dec="."){ + + if (sep=="tabulation") sep="\t" + if (sep=="semicolon") sep=";" + if (sep=="comma") sep="," + + # -- loading -- + data=read.table(file, header = TRUE, row.names=1, sep = sep, quote="\"", dec = dec, + fill = TRUE, comment.char="",na.strings = "NA") + + # -- acp / output pdf -- + resPCA =PCA(t(data),graph=graph, scale.unit=scale.unit) + # scale.unit=F : on réalise l'ACP sans la réduction des variables + # graph=F : pas de sortie graphique + dev.off() #close plot + dev.off() + + # -- output png -- + # Percentage of variance + png("percentage_of_variance.png", width =800, height = 400); + barplot(resPCA$eig$per,xlab="Components",ylab="percentage of variance"); + dev.off() + + png("eigenvalue.png", width =800, height = 400); + barplot(resPCA$eig$eig,xlab="Components",ylab="eigenvalue"); + dev.off() + + # -- output / return -- + system("zip -r acp.zip percentage_of_variance.png eigenvalue.png Rplots*.pdf", ignore.stdout = TRUE) +} + +listArguments = parseCommandArgs(evaluate=FALSE) +do.call(acp_metabolomics, listArguments)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_acp.xml Tue Jun 30 06:38:09 2015 -0400 @@ -0,0 +1,171 @@ +<tool id="abims_ACP" name="PCA" version="1.2"> + + <description>Principal Component Analysis using FactoMineR</description> + + <command interpreter="Rscript"> + abims_acp.r file "$input" graph TRUE scale.unit "$scale_unit" sep "$sep" dec "$dec" + </command> + + <inputs> + <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." /> + <!--<param name="graph" type="select" label="graph" help="if FALSE no graph generated"> + <option value="T" selected="true">TRUE</option> + <option value="F" >FALSE</option> + </param>--> + <param name="scale_unit" type="select" label="scale.unit" help="if FALSE no reduction of variables"> + <option value="T" selected="true">TRUE</option> + <option value="F" >FALSE</option> + </param> + + <param name="sep" type="select" format="text" optional="true"> + <label>Separator of columns</label> + <option value="tabulation">tabulation</option> + <option value="semicolon">;</option> + <option value="comma">,</option> + </param> + <param name="dec" type="text" label="Decimal separator" value="." help="" /> + + <!--<param name="nr_col_names" type="integer" label="names" value="2" help="number of the column with names of metabolits" /> + <param name="from" type="integer" label="from" value="15" help="number of the column starting peak values data (to exlude all metadata)" /> + <param name="to" type="integer" label="to" value="30" help="number of the column finishing peak values data (to exlude all metadata)" /> + <param name="gr_number" type="integer" label="gr_number" value="2" help="number of groups (conditions)" /> + <param name="nb_col_gr" type="text" label="nb_col_gr" value="8,8" help="number of column of each group; separate with coma as indicated; first position coresponding to the first group etc." /> + <param name="threshold" type="float" label="threshold" value="0.01" help="max adjusted p.value accepted" />--> + + </inputs> + + <outputs> + <data name="acp_zip" format="zip" from_work_dir="acp.zip" label="${input.name[:-4]}.pca.zip"/> + </outputs> + + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + + <help> + + +.. class:: infomark + +**Authors** Gildas Le Corguille ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr + +--------------------------------------------------- + +=== +PCA +=== + +----------- +Description +----------- + + +Performs **Principal Component Analysis (PCA)** with supplementary individuals, supplementary quantitative variables and supplementary categorical variables. +Missing values are replaced by the column mean. This scripts uses the FactoMineR package. + + +----------- +Input files +----------- + ++---------------------------+------------+ +| Parameter : num + label | Format | ++===========================+============+ +| 1 : Data Matrix file | Tabular | ++---------------------------+------------+ + + + +---------- +Parameters +---------- + +**Data Matrix file** + +Matrix of numeric data with headers (tabular format) issued from diffreport or annotateDiffreport to make post xcms analyse . + +**scale.unit** + +If FALSE: no reduction of the variables + +**Separator of columns:** + +Type of separator for the columns + +**Decimal separator:** + +Type of decimal separator of the numbers in your tabular files. + + + +------------ +Output files +------------ + + + +**input_name.pca.zip** + + | A zip file containing fours files (eigenvalue.png, percentage_of_variance.png, Rplots.pdf and Rplots1.pdf). + + +--------------------------------------------------- + + + +--------------- +Working example +--------------- + + +Input files +----------- + +**>A part of an example of Data Matrix file input :** + + ++--------+------------------+----------------+ +| Name | AN7 | AN8 | ++========+==================+================+ +|M102T645| 10880.0637170802 |17207.2222120537| ++--------+------------------+----------------+ +|M105T604| 41911.160863452 |38105.7953589089| ++--------+------------------+----------------+ + + + +Parameters +---------- + +| scale.unit -> **TRUE* +| Separator of columns: -> **tabulation** +| Decimal separator -> **.** + + + +Output files +------------ + + +**eigenvalue.png:** + +.. image:: pca_abims_eigenvalue.png + +**percentage_of_variance.png:** + +.. image:: pca_abims_percentage_of_variance.png + +**Rplots.pdf:** + +.. image:: pca_abims_Rplots.png + +**Rplots1.pdf:** + +.. image:: pca_abims_Rplots1.png + + + + + </help> + +</tool>