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kstreet13 / slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
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Running Multiple Times Results In Some Cells Not Plotting #208

Closed connerlambden closed 1 year ago

connerlambden commented 1 year ago

Hi, if I run slingshot once, everything is fine, but after running it again some cells are not plotting. Any ideas what might be causing this?

Screen Shot 2022-12-22 at 3 56 25 PM
connerlambden commented 1 year ago

After running slingshot, I'm plotting using: plot(reducedDims(sce)$UMAP, col = plotcol, pch = 16, asp = 1, main = plot_title)

kstreet13 commented 1 year ago

Hi @connerlambden,

My guess is that in the second plot, you are plotting the pseudotimes from a single lineage, hence why cells from the other lineage are not showing up. Also, in your first plot, it doesn't look like the colors match the trajectory (not sure why). And in both, the colors are continuous, so I'm not sure you actually colored by the cluster labels, as your code seems to intend.

Hope this helps! Kelly

connerlambden commented 1 year ago

Hi @connerlambden,

My guess is that in the second plot, you are plotting the pseudotimes from a single lineage, hence why cells from the other lineage are not showing up. Also, in your first plot, it doesn't look like the colors match the trajectory (not sure why). And in both, the colors are continuous, so I'm not sure you actually colored by the cluster labels, as your code seems to intend.

Hope this helps! Kelly

Thanks that worked! I ended up making separate plots for each lineage which helped clear things up.