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SCA-IRCM / SingleCellSignalR_v1

R package
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Formatting and plotting non-clustered Data #8

Closed oh111 closed 4 years ago

oh111 commented 4 years ago

Hi! I was wondering if the package had the capability of the following:

  1. Adjusting the formatting to label the clusters based of pre-set labels and other formatting (changing colors, thickness of arrows etc)
  2. Seeing cell signaling not based off clustering from the previous analyses (umap or tsne), but rather cell identity (without using cell markers). For instance if I have three cell lines-- control, cell 1 and cell2, can I use these in the signal analysis.

Thanks!

SCA-IRCM commented 4 years ago

Hi,

  1. No, the visualization parameters are not accessible in the visualize() function. However it could be a good idea in a further release. :)
  2. Yes, for that you just need to create a cluster vector of your own: cluster = c(rep(1, length(control.counts)),rep(2, length(cell1.counts)),rep(3, length(cell2.counts)))

Thanks for using SingleCellSignalR.

SCA