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cole-trapnell-lab / monocle3

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cell_stroke removal #609

Open legeinei123 opened 2 years ago

legeinei123 commented 2 years ago

Hi,

I recently re-downlaoded monocle3 and now in every plot_cells UMAP the cells of each cluster are shadowed by cell_stroke. I've tried to bring it down as much as possible and increase cell size/change colours, but it still looks awful. Is there anyway of removing this? It seems like the version I had didn't include the shading.

Thanks!

waltno commented 2 years ago

i'm a fan of cell stroke! my issue is that i want to keep it when i change color schemes. this may be able to help you!

plot_cells(cds, genes = "gene", scale_to_range = F , cell_size = 0.75)+scale_color_gradientn(colors=viridis(100))

shihsama commented 4 months ago

I found an approach to manage this problem. If you look at the structure of graph object, you'll find :

p1[["layers"]][[1]][["aes_params"]][["colour"]] [1] "black"

Since we have found this, it's easy to set:

p1$layers[[1]]$aes_params$colour <- 'transparent'

Fix it!!!