What software do you use to draw chromosomes with G-banding pattern and plot data alongside each chromosome? I'm interested in different kind of plots - lines, points, bars, etc - and high customization.

I have used coloredChromosomes.pl and chromosomeplot in MATLAB, but there are not enough features. What would you recommend to try?

UPDATE: I need something like this:

The quantsmooth Bioconductor package also has chromosome plotting functionality in the prepareGenomeplot(), paintCytobands() functions

Some Examples

EDIT: The code for these plots is quite involved, and depends a lot on the genomic data.

The supplementary data for Genome Res. 2007 17: 368-376, doi:10.1101/gr.5686107 contains the data and script to produce the figures for the paper, which also contain some of these ideograms

A quick example leads to the following plot

# prepareGenomePlot example
library(quantsmooth)
# construct genomic positions
CHR<-sample(22,40,replace=TRUE)  # Chromosomes
MapInfo<-lengthChromosome(CHR,"bases")*runif(length(CHR)) # position on chromosome
chrompos<-prepareGenomePlot(data.frame(CHR,MapInfo),paintCytobands = TRUE, organism="hsa")
# Chrompos returns a matrix with the positions of the elements on the plot
# You can use all kinds of base graphics functions to annotate the chromosomes
points(chrompos[,2],chrompos[,1]+0.1,pch="x",col="red")
# Show connection between 3rd and 4th element
segments(chrompos[3,2],chrompos[3,1],chrompos[4,2],chrompos[4,1],col="blue",lwd=2)

The GenomeGraphs package in Bioconductor allows to draw (human) chromosome ideograms with R. The package can be used to depict genome tracks of coverage, microarray measurements and genes together with the ideograms. See the user guide for an overview of different types of graphics. For the ideogram, the example looks like this (also in the GenomeGraphs paper):

Here is the code that makes something like this (from the user guide):

library(GenomeGraphs)
library(biomaRt)
data("exampleData", package = "GenomeGraphs")
mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
minbase <- 180292097
maxbase <- 180492096
genesplus <- makeGeneRegion(start = minbase,
                            end = maxbase, strand = "+", chromosome = "3",
                            biomart = mart)
genesmin <- makeGeneRegion(start = minbase,
                           end = maxbase, strand = "-", chromosome = "3",
                           biomart = mart)
seg <- makeSegmentation(segStart, segEnd,
                        segments, dp = DisplayPars(color = "black",
                                    lwd = 2, lty = "solid"))
cop <- makeGenericArray(intensity = cn,
                        probeStart = probestart, segmentation = seg,
                        dp = DisplayPars(size = 3, color = "seagreen",
                          type = "dot"))
ideog <- makeIdeogram(chromosome = 3)
expres <- makeGenericArray(intensity = intensity,
                           probeStart = exonProbePos,
                           dp = DisplayPars(color = "darkred",
                             type = "point"))
genomeAxis <- makeGenomeAxis(add53 = TRUE,
                             add35 = TRUE)
gdPlot(list(a = ideog, b = expres, c = cop,
            d = genesplus, e = genomeAxis, f = genesmin),
       minBase = minbase, maxBase = maxbase,
       labelCex = 2)

Edit: It supports multiple ideograms in one plot like this:

 ideog <- makeIdeogram(chromosome = 1)
 ideog2 <- makeIdeogram(chromosome = 2)
 ideog3 <- makeIdeogram(chromosome = 3)
 ideog4 <- makeIdeogram(chromosome = 4)
 gdPlot(list("1"= ideog, "2" = ideog2, "3" =ideog3, "4"=ideog4 ), 
 minBase = minbase, maxBase = maxbase)

If you plot data below the chromosomes using a base track, take care of the minbase, maxbase parameters because the chromosomes have different length!

Circos is very popular these days http://mkweb.bcgsc.ca/circos/

I found this bookmark in my del.icio.us

"Idiographica: a general-purpose web application to build idiograms on-demand for human, mouse and rat"

doi:10.1093/bioinformatics/btm455

http://www.ncrna.org/idiographica/

There is also gff2ps

Or you can use the custom tracks in the UCSC genome Browser.

This is exactly what UCSC genome graphs does: http://genome.ucsc.edu/cgi-bin/hgGenome

One more for people comfortable with R/BioC and looking for ways to plot various kinds of genomic data is ggbio. It extends the popular and powerful ggplot2 package from Hadley Wickham. It is highly flexible, integrates well with common Bioconductor objects like Granges, GenomicFeaures and has a great tutorial to get you started

You can try Flash GViewer. [?]I found it so nice that I tried to do a SVG version of it but not enough spare time to finish it.[?]

I am currently working on a project to visualize chromosomes.

Features:

1. annotate features with a very high resolution (up to nucleotide sized)
2. features are near in the sequence are near in the plot
3. exchangeable colormappings

I wonder if anyone sees an application?

Chromosome 12

Dear all, I would like to plot ideogram of zebrafish or stickleback. I tried some of your suggestions here. But they are mainly in human. Do you have any other suggestions? Regards, Nima