plotTranscript error

[kgaonkar6]

Hello,

Thank you working on this tool, it's quite useful. However, I've not been able to generate plots using plotTranscript using the master 2.53 version nor the devel branch for ATRX that has multiple transcripts in my ballgown input files from stringtie.

I'm using plotTranscripts(gene='MSTRG.50466', gown=bg2, meas='FPKM',samples = 'sample1', colorby='transcript') where 'MSTRG.50466 is the ATRX geneID from stringTie.
Error in smalldat[, colIndex] : incorrect number of dimensions

Using the same command I'm able to generate the plots from the examples. Is there something I've missed or is there a work-around?

[JMF47]

Can you run traceback() after the failed call so I can help narrow in on what line is throwing the error? Thanks!

[kgaonkar6]

Thank you for the quick response. Here is the command I'm trying to run:

plotTranscripts(gene='MSTRG.50466', gown=bg2, meas='FPKM',samples = 'sample1',colorby='transcript')
Error in smalldat[, colIndex] : incorrect number of dimensions

Running traceback() gives:

traceback()
2: closestColor(smalldat[, colIndex][which(t_id == tx)], colscale)
1: plotTranscripts(gene = "MSTRG.50466", gown = bg2, meas = "FPKM",
samples = "sample1", colorby = "transcript")