Questions tagged [umap]
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17 questions
1 vote
1 answer
134 views
Optimal PCA Dimensionality Reduction Before UMAP for 2D Visualization of High-Dimensional Data
I am working with scRNA data that I reduced to the 100 High Variance Genes and using UMAP to visualize it in 2D. Before applying UMAP, I perform PCA for dimensionality reduction. I am trying to decide ...
- 31
1 vote
1 answer
164 views
How can I quantitatively evaluate which UMAP is best in terms of clustering & embedding?
This question was also asked on Reddit I am new to sc-rna analysis, I have the dataset that I am trying to find out the best UMAP, experimented on trying out different values of the parameters as in (<...
- 11
4 votes
2 answers
614 views
Question about umap using different numbers of pca components as initialization
I am new to the scRNA-seq field and I have been doing some experiments of visualization of UMAP using different numbers of PCA components for initialization. The process involves projecting scRNA-seq ...
- 43
0 votes
1 answer
513 views
How to analyze hashtagged data with scanpy?
I used hashsolo to demultiplex my data and I am a bit confused as to how to continue the analysis. Following hashsolo my samples look like below: ...
- 145
1 vote
0 answers
720 views
How to plot average gene expression in scanpy?
I would like to make a UMAP where the cells are colored by the average expression of the bulk signature genes but I am not confident that I did it correctly. I would like to use scanpy for it. I did ...
- 145
2 votes
0 answers
245 views
How to make a UMAP for single cell data and color cells by average expression of a list of genes in scanpy?
I would like to make a UMAP where the cells are colored by the average expression of the bulk signature genes but I am not confident that I did it correctly. I would like to use scanpy for it. I did ...
- 145
1 vote
1 answer
218 views
1 vote
1 answer
980 views
How to get started with louvain/leiden algorithm with UMAP in R
A collegue of mine recently suggested to try the louvain algorithm for clustering multiplex cytometry data. However, implementations of louvain are kind of rare in R. To my knowledge the only stand-...
- 11
1 vote
0 answers
174 views
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 ...
- 2,242
0 votes
0 answers
4k views
DimPlot - How to highlight cells with identity colors?
I made this wrapper for DimPlot: ...
0 votes
1 answer
543 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
107 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 ...
- 2,239
2 votes
3 answers
2k 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 ...
- 31
0 votes
2 answers
3k 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. <...
- 391
1 vote
1 answer
187 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 ...
- 391