package circlize: How to extend circos plot?
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Brian Smith ▴ 120
@brian-smith-6197
Last seen 2.2 years ago
United States

Hi,

I wanted to use the 'circlize' package to make some genomic graphs. I wanted to follow the example given in the vignette/manual (https://jokergoo.github.io/circlize_book/book/initialize-genomic-plot.html - section 9.3)

tp_family = readRDS(system.file(package = "circlize", "extdata", "tp_family_df.rds"))

##   gene   start     end        transcript exon
## 1 TP53 7565097 7565332 ENST00000413465.2    7
## 2 TP53 7577499 7577608 ENST00000413465.2    6

circos.genomicInitialize(tp_family)


But this sets the beginning and end of the plot to the beginning and end of the exon coordinates. If I add a dummy exon to the data above, it will extend the plot, but will also show it as an exon.

My questions:

1. How can I modify the sample data to incude the 5' and 3' UTRs?
2. Also, how can I then extend the range for the gene such that the plot shows +/- 2kbp from the 5' and 3' ends?

thanks for your help!

circlize circos • 466 views
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Like I said on your biostars post, there is no use to adding the author's username (jokergoo) as a tag. It even has a bit of a negative connotation to it.