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hoelzer-lab / rnaflow

A simple RNA-Seq differential gene expression pipeline using Nextflow
GNU General Public License v3.0
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Representation of overlapping Sets, upsetr #10

Closed hoelzer closed 2 years ago

hoelzer commented 5 years ago

https://github.com/hms-dbmi/UpSetR

Cool instead of Venn diagrams

hoelzer commented 3 years ago

see also #86 this tool also implements UpSet plots as it seems

fischer-hub commented 2 years ago

@hoelzer Just to make sure I understand this correctly, for the UpSet plots we then are interested in the intersection of e.g. feature counts / expression above a certain threshold over the different contrasts? Or more the intersection of features in pathway groups? Or something else?

hoelzer commented 2 years ago

Hi @fischer-hub !

Yes exactly the first one. So the idea would be that we select significant DEGs based on some default thresholds, for example adj-p-value < 0.05 and log2FC > 1 for each contrast. Now, lets say we have three contrasts:

a) Mock b) Ebola-infected c) Marburg-infected

and do all pairwise comparisons that yield a certain number n of DEGs:

a-vs-b, n=50 a-vs-c, n=40 b-vs-c, n=10

Now, these three lists of gene IDs can be fed into UpSetR.

image

Does this make sense? The nice thing is, that this allows for multiple contrasts.

I have example code here for UpSetR: https://github.com/hoelzer/visual

fischer-hub commented 2 years ago

Ah okay! Great now its more clear to me, thx!