draw chromosome with genetic marker label

Question

[antibodyliu]

Hi everybody! I am a new guy in genomics. Now I want to draw a chromosome like this site provide. I need the neat chromosome and on the left the label of genetic markers, then on the right I want to label the QTL interval for Oryza Stavia. Can any one familiar with the drawing or any other tools I can utilize, please donnot hesitate to reply me. http://silico.biotoul.fr/pge/index.php

[Pierre Lindenbaum]

see Drawing Chromosome Ideograms With Data

Answer 1

[bernatgel]

If you can accept horizontal instead of vertical chromosomes, you can try with karyoploteR, an R package to plot data on genomes.

It uses UCSC to get cytoband data automatically and it's not available for Oryza Sativa so it will plot the chromosomes as gray boxes. If you have the coordinates for the cytobands, you can provide them to karyoploteR and it will use them to plot the chromosomes.

In R, if you have karyoploteR and BSgenome.Osativa.MSU.MSU7 installed, you can create a plot with this:

library(karyoploteR)

fake.qtls <- data.frame(chr=c("Chr1", "Chr1", "Chr3", "Chr7"),
                    start=c(10e6, 12e6, 15e6, 25e6),
                    end=c(18e6, 27e6, 17e6, 27e6))

kp <- plotKaryotype(genome="MSU7")
kpPlotRegions(kp, data=toGRanges(fake.qtls), col="#3423D2", layer.margin =0.2)

and it will create a plot like this.