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1 #!/usr/local/public/bin/Rscript --verbose
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2 # 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 # abims_hclust.r version 20130604
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8
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9 library(batch)
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10 library(ctc)
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11
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12 hclust_metabolomics = function(file, method = "pearson", link = "ward", normalization=TRUE, keep.hclust=FALSE, sep=";", dec="."){
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13
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14 if (sep=="tabulation") sep="\t"
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15 if (sep=="semicolon") sep=";"
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16 if (sep=="comma") sep=","
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17
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18 # -- loading --
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19 data=read.table(file, header = TRUE, row.names=1, sep = sep, quote="\"", dec = dec,
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20 fill = TRUE, comment.char="",na.strings = "NA")
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21
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22 # -- Normalization: logratio --
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23 if (normalization) {
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24 #meandata = apply(data,1,mean, na.rm=T)
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25 #data = log2(data/meandata)
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26 data=t(scale(t(data)))
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27 }
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28
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29 # -- hclust / output files for TreeView --
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30 file="hclust.cdt"
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31 hclust2treeview(data,file=file, method = method, link = link, keep.hclust= keep.hclust)
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32
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33 # -- output / return --
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34 system("zip -r hclust.zip hclust.*", ignore.stdout = TRUE)
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35 }
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36
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37 listArguments = parseCommandArgs(evaluate=FALSE)
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38 do.call(hclust_metabolomics, listArguments)
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