Different color of the same signal when plot all signals vs one signal in bubble plot

[Chrisdoan9]

Hi all,

May I know why the color of communication probability change when we plot all signals vs one signal? Is that color of each signal affect the overall color? In this case, when I plot all signals, the PGF2a-CBR1-PTGFA has no different between 2 conditions. However, when I plot only this signal, the color is very different. So I can conclude PGF2a-CBR1-PTGFA signal is different between 2 condition or not? Thank you so much!

[sqjin]

@Chrisdoan9 Yes, the colors are assigned based on the relative values in the plot. You can further check the expression levels of this L-R between the two conditions

[Chrisdoan9]

Hi @sqjin. Thank you for your help! I got it. Cellchat has this function to check gene expression but it is not directly compare between conditions plotGeneExpression(cellchat, signaling = "CXCL", enriched.only = TRUE, type = "violin")


It is hard to tell control (top figure) express more ligand-receptor gene than disease (bottom figure).

[Chrisdoan9]

Hi @sqjin, Happy New Year! Thank you so much for your kind support. Wishing you all the best in 2025!