Add labels to boxplot in QC_edgeR

[Rocio Nunez]

Add labels to boxplot in QC_edgeR:

Replace: boxplot(log2(data), main=paste("Boxplot of ",label," samples",sep=""),las=2, names=samplenames) for boxplot(log2(data), main=paste("Boxplot of ",label," samples",sep=""),las=2, names=samplenames, ylab="log2(counts)", xlab="Samples")

Replace: boxplot(log2(dgenorm$counts), col=boxcol, main=paste("Boxplot of ", label , " normalized samples",sep=""),las=2, names=samplenames) for boxplot(log2(dgenorm$counts), col=boxcol, main=paste("Boxplot of ", label , " normalized samples",sep=""),las=2, names=samplenames, ylab="log2(counts)", xlab="Samples")

[Rocio Nunez]

Añade también xlab=log10(counts) en los density plots:

plot(density(log10(data[,1])),col=boxcol[1],ylim=c(0,0.3), main=paste("Density plot of number of reads of ", label, sep=""), lwd=1.5)

plot(density(log10(dgenorm$counts[,1])),col=boxcol[1],ylim=c(0,0.5), main=paste("Density plot of normalized and filtered number of reads of ", label, sep=""), lwd=1.5)

[Rocio Nunez]

Sustituir en el heatmap:

heatmap(na.omit(as.matrix(dgenorm[sel,])),margins=c(10,8),main="Heatmap 250 most DE entities",cexRow=0.15,cexCol=0.5,labCol=samplenames)

Por

hmcol= colorRampPalette(brewer.pal(9, "YlGnBu"))(100) heatmap(na.omit(as.matrix(dgenorm[sel,])),margins=c(10,8),main="Heatmap 250 most DE entities",cexRow=0.15,cexCol=0.5,labCol=samplenames, col=hmcol)

[Eduardo Andres Leon]

Fixing issue #5 : Plot colors

→ <<cset 92f4121b3f36>>

[Eduardo Andres Leon]

Fixing issue #5 : Plot colors

→ <<cset 73a3bfcc882b>>

[Eduardo Andres Leon]

Fixing issue #5 : Plot colors

→ <<cset d0a044438fb0>>

[Eduardo Andres Leon]

QC_EdgeR.R, linea 221 y 222 :

#hmcol= colorRampPalette(brewer.pal(9, "YlGnBu"))(100) #heatmap(na.omit(as.matrix(dgenorm[sel,])),margins=c(10,8),main="Heatmap 250 most DE entities",cexRow=0.5,cexCol=0.5,labCol=samplenames, col=hmcol)