Closed ziyangliu93 closed 1 year ago
I almost forgot, under the situation I specify, I want to show circos plot for both A B and C.
Dear @ziyangliu93
If you are really not interested in a A vs (C+B) comparison (which would be an easy contrast/contrast_tbl definition as shown in the vignettes), I suggest running two separate MultiNicheNet analyses: one for A-vs-B and one for A-vs-C
Note that it does not make sense to wanting to show circos plots for all A, B and C if C would be involved in two different comparisons. You would need to make two different circos plots for C then.
Hi, thank you for your quick reply, because for my specific purpose, what I want to know is the interaction network differences in A, B and C under the same comparison settings. for example, for 10 same genes, there might be some interactions among gene 1 to gene 6 in group C (my control group), but the same interaction might occur also amongst gene 1 to gene 6 in group A and B, respectively, with different interaction strength and/or different interaction cell pairs. That is why I want to show 3 independent circos plots for A, B and C here. Looking forward to your reply.
In that case, I suggest running the analysis with the following settings. Then you compare A and B vs C separately, but you compare your control to both A and B
contrasts_oi = c("'C-(A+B)/2','A-C,'B-C'")
contrast_tbl = tibble(contrast = c("C-(A+B)/2","A-C", "B-C"), group = c("C","A","B"))
Note that the prioritization scores that are given as output should not be interpreted as interaction strengths, only as scores to rank interactions.
Hi, again, thank you for your kind and detailed suggestions, I will try to adjust my analysis code with your suggestions and see whether it suits my needs.
Hi, thank you for your nice work on this multinichenetr project. When I started using it, I encountered some problem. Here is what it is: I got a single-cell dataset consisting of 3 groups A, B and C. For my specific purpose, I want to compare A vs C and B vs C but no anything other comparisons. I wonder how should I set the contrast_oi and contrast_tbl in this situation.
Looking forward to your reply.