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Genes positioning on chromosomes
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3.5 years ago

How I can create a figure of Rice chromosomes to show the positions and locations of genes belong to a specific transcription factors family?

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18 months ago
bernatgel ♦ 1.9k
Barcelona, Spain

If you have the list of genes and their positions you can use the R package karyoploteR to create the plot (still in Bioconductor devel only, though). It can create karyoplots for various organisms including Rice. In this case you'll need to have the rice BSGenome package installed. Unfortunatelly since it relies on UCSC to get the cytobands and they are not available for MSU7, it will plot the chromosomes without banding. If you have this information youself you can provide it to karyoploteR.

library(karyoploteR)
library(regioneR)

#Create 50 regions as mock genes
genes <- createRandomRegions(50, length.mean=10000, genome="MSU7",non.overlapping = TRUE)
mcols(genes) <- data.frame(symbol=paste0("Gene", 1:50))

#Or read them from a BED file if available
#genes <- toGRanges("genes.file.bed")

kp <- plotKaryotype(genome="MSU7")
kpPlotRegions(kp, data=genes, r0=0, r1=0.3) #plot the genes
kpText(kp, data = genes, y=0.5, labels = genes$symbol, r0=0.3, r1=1, cex=0.5, srt=45) #and add the gene symbols

enter image description here

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