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cgao90 avatar cgao90 commented on July 21, 2024

Hi,

If you'd like to split the plot by time (Assuming each input dataset corresponds to one time point), you could try the following customized code:

library(ggplot2)
tsne_df <- data.frame([email protected]) # After running LIGER pipeline
colnames(tsne_df) <- c("Dim1", "Dim2") # e.g. tSNE or UMAP coordinates
tsne_df[['Dataset']] <- unlist(lapply(1:length(liger_object@H), function(x) {
  rep(names(liger_object@H)[x], nrow(liger_object@H[[x]]))
}))

p <- ggplot(data = tsne_df, aes(Dim1, Dim2, color=Dataset)) +
     theme_bw() + 
     theme_cowplot(12) +
     geom_point() + 
     labs(title = "Example Plot",
          x = "Dim1", y = "Dim2") + 
     facet_wrap(~ Dataset)
p

Hope it helps!

Best,

from liger.

samuel-marsh avatar samuel-marsh commented on July 21, 2024

As another option I have created package scCustomize that also has some Liger functionality. I have adapted the internal Liger plotting to support Seurat like arguments including split.by. You can check out functionality here: https://samuel-marsh.github.io/scCustomize/articles/LIGER_Functions.html

Best,
Sam

from liger.

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