Question: ggbio error when autoplot on PTPN11 gene
gravatar for Saad Khan
4.5 years ago by
Saad Khan330
United States
Saad Khan330 wrote:


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


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 :-


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.

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.







plots ggbio tracks • 1.8k views
ADD COMMENTlink modified 4.3 years ago by Giovanni M Dall'Olio26k • written 4.5 years ago by Saad Khan330
gravatar for Giovanni M Dall'Olio
4.3 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

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?

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Giovanni M Dall'Olio26k
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