Comments (2)
kstreet13
commented on July 21, 2024
Yeah, it looks like this is a display issue. When you run Slingshot, you seem to be using the PCA coordinates, but the plot uses UMAP coordinates. So the lineages are defined in the PCA space, which doesn't really line up with the UMAP space.
Also, I could be completely misunderstanding, but it sounds like your analysis goals may be similar to the ones described in this issue, which is an area of active development for us. Apologies if that's not helpful.
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GBeattie
commented on July 21, 2024
Ah silly me, I've fixed it now.
No that's great, makes for interesting reading.
Thanks!
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Related Issues (20)
- Is there any way that I could fit the NB-GAM for all the gene in my large dataset? HOT 1
- getCurves() Missing values HOT 8
- Curves and lineages HOT 3
- Error in igraph::shortest_paths(tree, from = l, to = ends, mode = "out", : At core/paths/dijkstra.c:360 : Weight vector must not contain NaN values, Invalid value HOT 3
- Average curve weights and Pseudotime HOT 1
- slingshot analysis on PCA but visualization on UMAP HOT 3
- how to analyze with 3 different treatments HOT 4
- how to calclate the POS to compare other algorithm? HOT 2
- Pulling and plotting Differential pseudotime data across different conditions/metadata slots HOT 1
- `embedCurves` should also map MST into new space HOT 1
- Slingshot followed by CellRank HOT 1
- is slingshot using only the variable genes? HOT 2
- Pick one lineage from many for conditiontest HOT 3
- How do I extract feature_info in my rds file? HOT 4
- What does a curve represent biologically? HOT 7
- Overlapping curve issue - change to code needed? HOT 3
- Removing a lineage from a `PseudotimeOrdering` object? HOT 3
- Error in graph.adjacency.dense: Adjacency matrix should be symmetric to produce an undirected graph. Invalid value HOT 5
- pseudotime in two lineage？ HOT 2
- Slingshot error HOT 1
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