Compare CCIs for more than two conditions

[zhanglab2008]

Hi team, I wonder if CrossTalkeR can be used to compare three conditions? Let's say, control, disease and treatment. Thanks!

[jsnagai]

Hi @zhanglab2008, in the current version you are able to compare more than one condition per time. Let's say that you have control, disease 1 and disease 2. You can use all the conditions in CrossTalkeR by passing the respective LR interaction List. We just ask you to be careful because the comparison always consider that the first position in the paths list is the control, it means that all the comparisons will be done using it as a reference. Because of that in the end the comparison in your result will be disease 2-control and disease 1-control.

[zhanglab2008]

Awesome! I will definitely try it out. Thanks!

[zhanglab2008]

Just tried it out. It works very well. Just one more question: how can I set the legend scale (for example, Weights, PageRank, etc) the same across multiple comparisons? I ask this because I want to compare the results from different comparisons ( e.g. Disease 1 versus Ctrl and Disease 2 versus Ctrl, to see which disease altered the cell cell communication more). Thanks for developing this timely algorithm indeed. I like it a lot!

[jsnagai]

@zhanglab2008 sorry for the late reply, you should be able to do it using the data object and the emax parameter in the plot_cci function.