Genes positioning on chromosomes

Question

[israr.unimi]

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

[Pierre Lindenbaum]

see

• Visualizing the position of many genes a time
• Drawing Chromosome Ideograms With Data
• Representing A Feature Along The Length Of The Chromosome
• Normalized coverage histograms for selected chromosome region
• Visualizing Genes On A Chromosome According To Their Position
• How To Draw Genome Features Along Chromosome

Answer 1

[bernatgel]

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