Question: Problems drawing cytobands with karyoploteR
1
gravatar for uxiavb
19 months ago by
uxiavb10
uxiavb10 wrote:

I am working with karyoploteR to represent DEG. I am working with the pombe genome, so I created a custom genome with karyoploteR. But when I try to add the centromeres as cytobands, only the centromeres are represented. Here below is the code I used:

custom.genome <-toGRanges(data.frame(chr=c("I", "II", "III"), start=c(1,1,1), end=c(5579133,4539804,2452883)))
custom.cent <- toGRanges(data.frame(chr=c("I", "II", "III"), start=c(3753687,1602264,1070904), end=c(3789421,1644747,1137003), name=c("cent", "cent", "cent"), gieStain = c("stalk", "stalk", "stalk")))

When I don't use the centromeres information I get the chromosomes:

kp <- plotKaryotype(genome=custom.genome)

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But when I used the centromeres information, only the centromeres are represented:

kp <- plotKaryotype(genome=custom.genome, cytobands = custom.cent)

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I am not really sure why it is not working. I was following a package tutorial. Thank you beforehand, Alicia

rna-seq bioconductor R • 608 views
ADD COMMENTlink modified 19 months ago by zx87549.7k • written 19 months ago by uxiavb10
2

Very nice formatting question, with examples and figures, well done !

I guess that you found a bug in karyoploteR, when the custome.genome display is removed when you add custom.cytobands

I suggest you to open a new issue to bernatgel github : https://github.com/bernatgel/karyoploteR/issues

ADD REPLYlink modified 19 months ago • written 19 months ago by Bastien HervĂ©4.8k
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