I have posted a similar question here : http://www.biostars.org/post/show/46740/how-to-create-such-figure-of-chromosomes/#46762
An other similar figure representing multiple samples ideograms can be found here : http://www.biostars.org/post/show/378/drawing-chromosome-ideogams-with-data/
From mouse genome mm9 I have CNV Losses and Gain from Breakdancer and CNVnator, so our data have only :
- type of CNV
- breakpoint start and end coordinates
- chromosome number
- length of the Copy Number.
Based on those data and knowing that we have 6 samples to represent on one ideogram, which software is more appropriate to have a nice ideogram of our 6 samples ?