lmcinnes / lmcinnes/umap

UMAP plot points gathered at edge of axes

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Python
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Description

Hello,

I am trying to run UMAP via RStudio and I seem to have a scaling issue when trying to plot UMAP1 versus UMAP2. I've attached the plot below for your review.
I used 8 metaclusters via this command:

> cell.dat <- run.flowsom(cell.dat, cluster.cols, meta.k = 8)

![Factor plot - FlowSOM_metacluster - plotted on UMAP_X by UMAP_Y](https://user-images.githubusercontent.com/91157410/135117888-340cd554-d784-4f19-ae35-ccc464b2ce84.png)

Please let me know if any other information is needed to solve.

Thank you in advance for any suggestions!

Best,

Kayla

Contributor guide

Open the contributing guide

Research direction

Start by reviewing the reported RStudio command `cell.dat <- run.flowsom(cell.dat, cluster.cols, meta.k = 8)` and the attached UMAP1-versus-UMAP2 plot. Determine whether the edge clustering is reproducible and whether the report contains enough information to identify a UMAP or FlowSOM scaling problem; completion requires a reproducible diagnosis or a clearly scoped fix.

Written by the indexing model from the issue text.

Assessment

Tech stack
python, r
Domain
data-visualization, machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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