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1 #!/usr/local/public/bin/Rscript
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2 # abims_acp.r version="1.1"
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3
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4 # date: 04-06-2013
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5 # **Authors** Gildas Le Corguille ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr
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6
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7
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8
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9 #function PCA from package FactoMineR
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10
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11 library(batch)
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12 library(FactoMineR)
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13
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14 acp_metabolomics=function(file ,graph=FALSE, scale.unit=TRUE, sep=";", dec="."){
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15
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16 if (sep=="tabulation") sep="\t"
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17 if (sep=="semicolon") sep=";"
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18 if (sep=="comma") sep=","
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19
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20 # -- loading --
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21 data=read.table(file, header = TRUE, row.names=1, sep = sep, quote="\"", dec = dec,
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22 fill = TRUE, comment.char="",na.strings = "NA")
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23
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24 # -- acp / output pdf --
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25 resPCA =PCA(t(data),graph=graph, scale.unit=scale.unit)
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26 # scale.unit=F : on réalise l'ACP sans la réduction des variables
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27 # graph=F : pas de sortie graphique
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28 dev.off() #close plot
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29 dev.off()
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30
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31 # -- output png --
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32 # Percentage of variance
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33 png("percentage_of_variance.png", width =800, height = 400);
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34 barplot(resPCA$eig$per,xlab="Components",ylab="percentage of variance");
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35 dev.off()
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36
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37 png("eigenvalue.png", width =800, height = 400);
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38 barplot(resPCA$eig$eig,xlab="Components",ylab="eigenvalue");
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39 dev.off()
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40
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41 # -- output / return --
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42 system("zip -r acp.zip percentage_of_variance.png eigenvalue.png Rplots*.pdf", ignore.stdout = TRUE)
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43 }
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44
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45 listArguments = parseCommandArgs(evaluate=FALSE)
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46 do.call(acp_metabolomics, listArguments)
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