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SCA-IRCM / SingleCellSignalR_v1

R package
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Hot to plot interactions between two groups of cells comprising different cell types? #2

Closed kaizen89 closed 4 years ago

kaizen89 commented 4 years ago

Hi, Thanks for making this great tool. I was wandering if there was a way to to plot interactions between two groups of cells comprising different cell types like in this example here where I plotted the interactions between immune and stromal cells. Thank you image

SCA-IRCM commented 4 years ago

Hi, Thanks to you for using it! I don't fully understand your question, I think you want to use the visualize() function. You'll find more details about how to use it in the User's Guide (https://github.com/SCA-IRCM/SingleCellSignalR_v1/blob/master/UsersGuide.html). Keep me posted if you have any other question. Thanks again.

SCA

kaizen89 commented 4 years ago

I will try to rephrase, Let's say I have dataset comprising immune cells and stromal cells, the cluster 1,2 and 3 are different immune cell populations and the clusters 4,5 and 6 are different stromal cell populations. What I want is to focus the analysis of the pairs between each of the immune cells and each of the stromal cells. Is this something that is currently possible or should I specifiy each of the combinations (1,4), (1,5), (1,6), (2,4), (2,5), (2,6) etc. The problem is that I have 100 possible combinations. Hope it is more clear now.

SCA-IRCM commented 4 years ago

Once you have the signal list (output of the cell_signallling() function), you can select the elements you want the visualize() function to plot. There is no systematic way to do it but you can use the names of the signal list. For example signal[grepl("immune", names(signal))] will select only the elements of signal that involve immune cells.

SCA-IRCM commented 4 years ago

Hope this helps. :)