Hello,
when plotting the exon expression for a gene using the DEXSeq package two problems arise:
1. Since my gene has >20 exons and the first and second exons being far away from the others, the gene model plot below the expression plot shows very thin exons and long introns. How can I reduce the size/width of the introns in the plot? Is it possible to subset the data in order to plot only e.g. exons 3-18?
2. Additionally my gene is on the - strand, which means that the order of the exons in the expression plot is from left to right, but the order of the exons in the gene model is from right to left (according to the strand). How is this fixable?
I use the method described in the manual:
plotDEXSeq(dxr1, "gene_id", displayTranscripts = TRUE, legend = TRUE, lwd = 2, cex=1.3, cex.axis=1.2)
Thank you!!
I found a temporary solution (which works only for visualization): Editing the coordinates in the gff file to small numbers (and changing the strand specifity) can give a nicer output. I would not recommend if doing multiple plots..