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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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Want to add motif corresponding to peaks in Coverage Plot #1552

Closed raunakkar closed 10 months ago

raunakkar commented 10 months ago

Hi @timoast, Thank you for this wonderful package. I am very naive in this field and was looking for some guidance as to how to add motifs in a coverage plot? I have paired (ATAC + RNA) multiome data and have added Motif object to my dataset. However I want to annotate a peak as a putative TF binding site and visualize in Coverage plot. Something similar to this (doi: https://doi.org/10.1016/j.xgen.2023.100263) : Screenshot from 2023-12-09 14-44-29 For now I have coverage plots like this: coverage_GNLY.pdf Any suggestions would be amazing.

Thank you in advance.

timoast commented 10 months ago

Hi, you can set the region.highlight parameter and give the coordinates of the motif position that you want to highlight

raunakkar commented 10 months ago

Thank you for the prompt response @timoast . Unfortunately not exactly what I am looking for. What I am looking for is some way to annotate the set of peaks for their motif enrichment de novo, rather than manually annotating them. Like had there been a parameter in the coverage plot where I can supply the motif file and the set of peaks in the region would be annotated for motif enrichment. I don't know if this makes sense? Please do correct me if I am wrong.

Thank you.