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Why umap give ill-defined and unclear clusters result? #2024

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Sophia409 opened this issue Aug 26, 2019 · 1 comment
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Why umap give ill-defined and unclear clusters result? #2024

Sophia409 opened this issue Aug 26, 2019 · 1 comment
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@Sophia409
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@andrewwbutler hello,
My cell number is about 50 thousand.So i think my resolution 0.6 is not excessive.And I find when I use tsneplot to show it ,the clusters separate well and cluster 21 gather together.But in the umap, cluster 21(pink dots) is really scattered. So what's the reason?How can I make these clusters separate well on the umapplot? Because umap can show better connectivity and the relationship among these clusters, I prefer to use it not tsne.
#1991 (comment)

tsne plot
image
umap plot
image
@andrewwbutler
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Hi,

There are a number of factors that influence the UMAP results. You can consider the PCs that are included and how many/which features are used as input to the PCA. There are also a number of UMAP-specific parameters that you can play with. See this document or the help (?RunUMAP) for a more thorough discussion of some of those parameters.

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@andrewwbutler @Sophia409