Questions tagged [umap]

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Different colors in UMAP

I have integrated top ten TCR clones into Seurat object something like below You are seeing some clones are expressed in more than one cells So in Seurat I have something like ...
  • 1,707
0 votes
0 answers
706 views

DimPlot - How to highlight cells with identity colors?

I made this wrapper for DimPlot: ...
0 votes
1 answer
97 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 ...
  • 101
1 vote
1 answer
46 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 ...
  • 2,099
2 votes
3 answers
723 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
2 answers
2k 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. <...
  • 319
1 vote
1 answer
125 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 ...
  • 319
0 votes
2 answers
493 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
1 answer
4k views

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

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