switchPlot() does not show all isoforms

[John Smout]

Hi,

Follow up question to my previous question. As mentioned before, I'm using isoformSwitchAnalyser with per-isoform q-values imported from an independent analysis using DEXSeq and StageR. I'm doing this because running DEXSeq within isoformSwitchAnalyseR did not give me any genes with evidence of DTU, for some reason, although running DEXSeq separately did. The fact that I am importing an external analysis could be relevant to the issue I'm having here.

I am trying to use switchPlot() to visualise differences between transcripts in my experiment, and I thought I had cracked it, but it seems that I'm still having issues.

I have two different switchAnalyserLists for two different comparisons. I noticed that when I call switchPlot() on the same gene from both lists, one shows 4 isoforms and the other shows 5. After a bit of digging I found that there are 7 isoforms listed in each of the switchAnalyzerList (under mySwitchList$isoformFeatures), so actually both plots are missing transcripts. Weird!

The manual page states that switchPlot should show all transcripts for a given gene, if called using the gene name. Obvioulsy, though, I am not following the standard usage so perhaps something unexpected has happened?