added remove.isolate, keep color consistency, return vertex.receiver …

[alperdomo]

…steps

[alperdomo]

Dear Suoqin Jin,

One of the most used functions in currently published works using cellChat is netAnalysis_signalingRole_network().

We added the remove.isolate functionality to deal with data sets containing many cell states that do not display signaling roles, so the heatmap does not look quite empty where only a handful of cells display roles for an interesting pathway. For instance, if a data set has > 70 cell states, as the ones I handle. To preserve the color code across multiple pathways analyses within a single dataset, across datasets with the same cell states, but also across other functions from CellChat, for instance, netVisual_chord_gene(), the remove.isolate step was added after checking if is.null(color.use).

We additionally added one step to enable the return of the vertex.receiver indexes that are used in other functions from CellChat, for instance, netVisual_aggregate().

Best regards,

Alvaro