Plotting HiChIP data without Sushi in R

Question

[Morgan]

Hello. I am pretty new to the programming world and need a bit of help with plotting HiChIP data. The tutorial for HiChIP (https://hichip.readthedocs.io/en/latest/plot_arc.html) is out of date and I have gotten all the way up to plotting the data on my own but the package Sushi is no longer in use. The tutorial is having me use Sushi for the following commands "plotBedgraph" and "plotBedpe". Any advice with other packages/commands to use instead of Sushi?

as a note, when going to Sushis GitHub, it says PlotGardener is the go to now, however it seems like plotgardener doesnt do much for bedgraphs. Thanks!

[Matthias Zepper]

I used the Gviz packageto plot genomic regions for my thesis in R. However, despite many default TrackClasses, the library lacked means to represent genomic interactions such as those of cis-regulatory elements with promoters.

Therefore, I had to tweak the package to display arcs. Fortunately, Gviz contains an AlignmentsTrack class, which allows to render BAM files directly. This class supports to display gapped alignments as sashimi plot: Gaps are spanned by connecting lines, the breadth of which is chosen relative to the number of reads supporting the respective gap.

This feature could be diverted to display interactions. For this purpose, I wrote a custom function that accepts a BED file containing the coordinates of two interacting genomic fragments as input and simulate gapped reads bridging those positions. The resulting fake read alignments were reformatted to the internal Gviz format and displayed alongside the other data.

Maybe you can use a similar approach for your HiChIP data?

Answer 1

[Morgan]

Hello! Thank you for your answers, I have decided to use a mix of the WashU genome browser and the python package CoolBox. Thank you all again!