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10
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1 # pairwiseScatterPlots
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2 # scatter plots for pairwise comparaisons of log counts
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3
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4 # input : counts, target, outputName
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5 # output : scatter plots (pdf: allows multiple figures in one file)
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6
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7 # created Feb 21th, 2012
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8 # modified Sept 27th, 2012 (pdf output file)
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9 # modified Oct 30th, 2012 (png)
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10 # Marie-Agnes Dillies
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11
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12
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13 pairwiseScatterPlots <- function( counts, target, OUT_scatterPlot, out = TRUE, pdffile = FALSE ){
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14
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15 if (out & !pdffile) png( OUT_scatterPlot )
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16 if (pdffile) pdf( OUT_scatterPlot )
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17
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18 conds <- unique(target$group)
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19 # colnames(counts) <- target$label
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20
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21 for (i in 1:(length(conds)-1)){
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22 for (j in (i+1):length(conds)){
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23 cond1 <- conds[i]; cond2 <- conds[j]
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24 pairs( log2(counts[, which(target$group %in% c(as.character(cond1), as.character(cond2)))]+1),
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25 pch=".", cex=0.5, main = paste(cond1, cond2, sep=" vs ") )
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26 }
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27 }
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28
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29 if (pdffile) dev.off()
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30 if (out) dev.off()
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31 }
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