ggbio error when following tutorial, ideogram not highlighted, genetrack not working
0
0
Entering edit mode
gpwhiz ▴ 10
@gpwhiz-19034
Last seen 6.0 years ago

Hello,

I am trying to follow ggbio'stutorial, however I am getting errors on the following

1) When plotting the Ideogram, the region does not get highlighted

I am using the following code

p.ideo <- Ideogram(genome = "hg19")
p.ideo

p.ideo + xlim(GRanges("chr2", IRanges(1e8,1e8+100000)))

I also tried the following, but that also didnthighlight the region

abc <- GRanges("chr1", IRanges(1e8,1e8+10000000))

Ideogram(genome = "hg19", xlabel = TRUE, color = "blue",
         fill = "green",which = abc)

2) When trying  to plot the gene region,

I used the following

library(ggbio)
library(Homo.sapiens)
class(Homo.sapiens)

data(genesymbol, package = "biovizBase")
wh <- genesymbol[c("BRCA1", "NBR1")]
wh <- range(wh, ignore.strand = TRUE)
p.txdb <- autoplot(Homo.sapiens, which  = wh)

I get the following error

Parsing transcripts...
Parsing exons...
Error in `rownames<-`(`*tmp*`, value = c("61241", "61242", "61243", "61244",  : 
  invalid rownames length

 

Any help will be appreciated.

ggbio ideogram autoplot • 1.0k views
ADD COMMENT

Login before adding your answer.

Traffic: 390 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6