ggbio error when autoplot on PTPN11 gene

Question

[Saad Khan]

Hi

I was wondering if any of you has used "ggbio" before. I was going through its manual and for some of the examples I can not make it work with certain genes. In my case I was trying to use it with "PTPN11" gene using the following code

library(ggbio)
library(GenomicRanges)
library(BSgenome.Hsapiens.UCSC.hg19)
library(biovizBase)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(VariantAnnotation)
library(Homo.sapiens)

data(genesymbol, package = "biovizBase")

wh <- genesymbol['PTPN11']
 p.txdb <- autoplot(Homo.sapiens, which = wh)

It throws the following error

gap" is not matching to following arbitrary model terms"cds CDS Cds exon EXON Exon utr UTR Utr"

Constructing graphics...
Error in `[[<-`(`*tmp*`, name, value = 1L) : 
  1 elements in value to replace 0 elements
Calls: apply ... <Anonymous> -> .local -> .hackFun -> $<- -> $<- -> [[<- -> [[<-
Execution halted

In some forums I have found that installing new version of ggbio could solve the problem. But I am unable to do so using :-

library(BiocInstaller)
useDevel()

or downloading the svn repository using svn checkout tarring it and installing it using R CMD INSTALL.

I have tried mailing the author but I have not heard from him yet. This is the graph that gets generated using full code that I have. It works for certain genes and not for others.

https://drive.google.com/file/d/0B9g-QPZ8EqmUMjJzRElTTWZIaGM/edit?usp=sharing

I was wondering if somebody has dealt with this ggbio problem before and suggest possible solutions regarding the same.

Also if there is a better way to do the same.

Thanks

Answer 1

[Giovanni M Dall'Olio]

I tried the same code on my computer and it works. I also got a warning about the gap model, but not the error about about replacing 0 elements. My version of ggbio is 1.14.0, so you don't need to install the development version. Which version of ggbio are you using? Have you tried running the code on a clean environment, without other variables or packages loaded?