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 :-
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.