Drawing yeast chromosome ideograms with data

Question

[marco.di.distefano.1985]

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

Answer 1

[bernatgel]

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")

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)

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