Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Making a ligand-receptor-target circos plot #20

Open
abberclark opened this issue Apr 8, 2020 · 2 comments
Open

Making a ligand-receptor-target circos plot #20

abberclark opened this issue Apr 8, 2020 · 2 comments
Labels
enhancement New feature or request

Comments

@abberclark
Copy link

Thanks for this great package!

I would like to make a ligand-receptor-target circos plot as described in the "circos" vignette and as seen in "B":
circos plot with summary

I can make both ligand-target and ligand-receptor circos plots, but it's unclear how to overlay the plots. My question is how do you know which target genes are associated with a particular receptor (i.e., align the target genes and receptors for the receiver cell)?

@browaeysrobin
Copy link
Member

Hi @abberclark,

In the example you showed, we plotted the outer layer of receptors without 'really' taking into account the corresponding target genes per receptor. What we did was dividing the target genes in 3 groups: mainly Csf1-regulated targets, Bmp/Dll-regulated targets, and targets of 'other' top-ranked ligands. All Csf1-regulated targets were then plotted under the Csf1 receptor, all Bmp/Notch-regulated targets were plotted under all expressed receptors for the specific Bmps and Dlls, but we do not infer links between specific receptors and specific targets. So if you see that e.g. Myc is under Notch1, this does not mean that the only receptor upstream of Myc is Notch1, but just that Myc was classified to belong to the group of targets genes downstream to the group of ligands of which at least one ligand has Notch1 as receptor. For the third group, there is even less correspondence, here we just plotted all 'other' targets under all 'other' receptors.

So currently, you cannot use this approach to make a ligand-receptor-target plot with real correspondence between receptors and targets. Sorry for not being able to help you really out. To check real correspondence between ligand-receptor-target, I would suggest using the heatmap visualizations.

In the future, I might look for a solution to this because the circos plot is a beautiful visualization, but it seems hard to do and is not really a priority right now.

@Victor-K27
Copy link

Hi @browaeysrobin

Just to confirm, this annotation of genes under the receptors was manual right? Or did you generate it programmatically?
Thanks,
Victor

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

3 participants