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18
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1 # majSequence
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2 # compute proportion of reads associated with most expressed sequence
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3
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4 # input : counts, target, projectName
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5 # output : barplot, % associated with majority gene
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6
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7 # created Feb 7th, 2012
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8 # modified Feb 20th, 2012
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9 # modified April 30th, 2012
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10 # Marie-Agnes Dillies
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11
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12
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13 majSequence <- function( counts, group, OUT_majSequenceName, out = T, position = "topright" ){
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14
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15 if (out) png( file=OUT_majSequenceName )
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16
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17 maj <- apply(counts, 2, function(x){x <- x[order(x, decreasing=T)]; x[1]*100/sum(x)})
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18 seqname <- apply(counts, 2, function(x){x <- x[order(x, decreasing=T)]; names(x)[1]})
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19
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20 x <- barplot( maj, col=as.integer(group)+1, main = "Proportion of reads from most expressed gene",
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21 ylim = c(0, max(maj)*1.2), cex.main=0.8 )
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22 for (i in 1:length(seqname)) text( x[i], maj[i]/2, seqname[i], cex=0.8, srt=90, adj=0)
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23 legend( position, as.character(unique(group)), lty=1, col=as.integer(unique(group))+1 )
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24
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25 if (out) dev.off()
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26 }
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