Questions tagged [umap]

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1answer
45 views

Using different "principal components" in UMAP visualizations

In certain UMAP visualization, it appears that the visualizations show the first UMAP "principal component" plotted against the second. For example, like this: Apparently, this lets us use ...
1
vote
1answer
33 views

Is there a difference between any scRNA-seq visualization and pseudotime?

Is there a good definition of pseudotime? Some tools are clearly labeled as pseudotime and produce values along a trajectory, but there are more complex approaches that involve branching and ...
2
votes
3answers
500 views

umap and Louvain clustering on normalized data

I know that scaled data must be used for PCA for example as it is based on variance maximization. However I'm wondering if it's the same case for UMAP ? If the data are single-cell RNA seq, after ...
0
votes
2answers
1k views

Adding certain barcodes to metadata in Seurat

I want to upload an excel file sheet that has certain barcodes that I would like to show on my umap. How do I go about adding the file and linking it to the metadata? Below is my following code. <...
1
vote
1answer
108 views

umap highlighting two different models

I'm trying to create a umap for single cell data from human samples and ptx samples. I can get the umap to where it shows the umap with the different clusters but I want to show where the ptx samples ...
0
votes
2answers
468 views

Running python script from terminal: umap issue

Some time ago I asked the question: RunUMAP in Seurat not working: module 'umap' has no attribute 'UMAP' It was solved by following the answer in it, however, it is still not ...
3
votes
1answer
3k views

RunUMAP in Seurat not working: module 'umap' has no attribute 'UMAP'

I am trying to run UMAP in the following way: ...