search

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
117 stars 14 forks source link

Redundant Comparison Shown #84

Open DarioS opened 2 months ago

DarioS commented 2 months ago

I have a variable with two conditions. How to do an analysis of Yes-No, but not No-Yes? I want to avoid the redundant heatmap.

contrasts_oi = "'Yes-No'")
contrast_tbl = tibble(contrast = "Yes-No", group = "Yes")
Error in multi_nichenet_analysis(allHuman, "cellType", "samples", characteristic,  : 
  conditions written in contrasts_oi should be in the condition-indicating column! This is not the case.

image

One column is the mirror image of the other column and is unnecessary. Also AREG-EGFR has no difference between Up, Down. Why?

browaeysrobin commented 2 months ago

Hi @DarioS

Normally, you can do an analysis with only "Yes-No". The error message you got here is probably because of a typo in the contrast definition: contrasts_oi = "'Yes-No'") instead of contrasts_oi = ("'Yes-No'").

However, the main issue is the redundancy in the plot. Therefore, we will flag this issue as "enhancement" to add more flexibility in the plotting function to give users the option to make this plot non-redundant in case of 2 conditions.