Visualizing TF accessibility for eRegulons

[tu4n-p]

Hi, I was wondering if there's anyway I could visualize TF accessibility ( just like what the software did for TF expression/Target gene expression/region accessibility with UMAP/tSNE) for eRegulons of interest?
Thank you!

[SeppeDeWinter]

Hi @tu4n-p

What do you exactly mean with TF-accessibility? You can visualise the accessibility of the target regions using the AUC-values, but I don't think this is what you're looking for?

Best,

Seppe

[tu4n-p]

Hi @SeppeDeWinter , sorry about the confusion. I guess what I meant is TF gene accessibility/differentially accessible TF genes, not the target genes . In the human cerebrium tutorial, it plotted something like this. So I was wondering if I can also plot PRRX_2 accessibility on the same UMAP as well.
Thanks,

[SeppeDeWinter]

Hi @tu4n-p

I'm still not entirely sure what you mean exactly?
Do you mean like this: https://pycistopic.readthedocs.io/en/latest/Single_sample_workflow-RTD.html#12.-Gene-activity ?

Best,
Seppe

[tu4n-p]

Yes! That's what I meant. Sorry about the wording.

[SeppeDeWinter]

It is possible to show these values on the same UMAP, however we don't directly have a function for it.

It should be trivial however to write some custom code to show this. I would suggest having a look at this function for reference:

scenicplus/src/scenicplus/dimensionality_reduction.py

Line 717 in 0173233

def plot_AUC_given_ax(

Hope this helps.

best,

Seppe

[tu4n-p]

Perfect. Thanks for the rapid response!