Drawing yeast chromosome ideograms with data
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Entering edit mode
5.7 years ago

Dear all,

I was looking for tools which allow to draw S cerevisiae chromosomes' with data. So far I found prepareGenomePlot() in R which allows to do it for human and mouse karyotypes or biocircos which allows to represent karyotypes on a circle.

Are there other tools to represent yeast chromosomes in a linear shape with data, similarly to what prepareGenomePlot() allows to do for human and mouse chromosomes?

Thanks, Marco

yeast chromosome ideograms • 2.6k views
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4.2 years ago
bernatgel ★ 3.2k

Hi Marco,

If you are still interested in this, I would suggest you to try karyoploteR, it's an R/Bioconductor package to plot genomes (and parts of them) with data. And most importantly, its not tied to any predefined genome.

You can use any of the pre-loaded genomes such as S cerevisiae (in this case, the "sacCer3" genome assembly) and create a plot with

library(karyoploteR)
kp <- karyoploteR::plotKaryotype(genome = "sacCer3")

enter image description here

and then add data into it with kpPoints, kpSegments, kpRect... or more specialized functions to plot regions (kpPlotRegions) or genes (or other markers) (kpPlotMarkers), etc...

genes <- toGRanges(c("chrI", "chrI", "chrX"), c(100e3, 110e3, 600e3), c(101e3, 111e3, 601e3), c("Gene1", "Gene2", "Gene3"))
names(mcols(genes)) <- "labels"
kp <- karyoploteR::plotKaryotype(genome = "sacCer3")
kpAddBaseNumbers(kp, tick.dist = 100e3)  
kpPlotMarkers(kp, genes, labels=genes$labels, text.orientation = "horizontal")
kpRect(kp, chr="chrVII", x0=400e3, x1=800e3, y0=0, y1=1, col="#FFAAAAAA", border=NA)

enter image description here

You can find more information on the available plotting function either in the package vignette or in the karyoploteR examples and tutorial page.

In that page you can also find a specific tutorial on how to use karyoploteR with custom genomes in case you need to work with an organism with no genome available in the form of a BSgenome.

Hope this helps

Bernat

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