Plotting DNA overlaps considering signal density

Question

[bioinfo456]

Hi all,

Which platform and package could be used to plot the graphs as mentioned in the following page?

Answer 1

[Alex Reynolds]

I used R and ggplot/geom_rect to make those plots.

Here is a copy of the script. The title property (on lines 45, 64, 83, and 102) corresponds to plots linked on the page your question is pointed to, and you can use the demo downloads available from the bottom of the BEDOPS bedmap docs page to get to BED files to use as input, to recapitulate those plots:

Here is the Makefile used to call it:

https://github.com/bedops/bedops/blob/master/docs/assets/reference/statistics/Makefile

[bioinfo456]

Thank you so much :).