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saeyslab / multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
GNU General Public License v3.0
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How to set "contrast_tbl" to reproduce Fig 3a #57

Closed haotian-zhuang closed 6 months ago

haotian-zhuang commented 6 months ago

Dear Robin @browaeysrobin,

Thank you for the great tool. To reproduce the Fig 3a of the breast cancer example, I wonder how to set the "group" column in the "contrast_tbl"? The vignette uses the following setting, but is this the same setting to generate the Fig 3a? Thanks!

contrast_tbl = tibble(contrast = c("(OnE-PreE)-(OnNE-PreNE)", "(OnNE-PreNE)-(OnE-PreE)"), group = c("OnE","OnNE"))

browaeysrobin commented 6 months ago

hi @haotian-zhuang

Yes, that was indeed the setting we used for the paper.

haotian-zhuang commented 6 months ago

Hi Robin @browaeysrobin,

Thank you for the prompt reply! Could you explain more why setting group = c("OnE","OnNE")) for Fig 3a? For example, why setting group = "OnNE" represents the "Interactions that increase during therapy in patients without expansion"?

And if keeping the "contrast" but setting group = c("OnE","PreE")), for example, how to interpret the two figures drawn?

Thanks!