Question: ggbio error when following tutorial, ideogram not highlighted, genetrack not working
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gravatar for gpwhiz
9 months ago by
gpwhiz10
gpwhiz10 wrote:

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.

ideogram ggbio autoplot • 217 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by gpwhiz10
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