scverse / scverse/scanpy

why umap showing bbknn perfectively integrated but tsne

Open
#1,370 5 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Python
Stars
2.6k
Forks
779
Avg merge
1d 4h
Merged PRs (30d)
27

Description

Hi @all,
Thanks to develop the great tools,
I encounter a pecular problem on bbknn integrated data.
i follow the workflow code to run the data integrated,the code showing below,

 sc.pp.highly_variable_genes(adata)

adata = adata[:, adata.var['highly_variable']]
sc.tl.pca(adata, svd_solver='arpack')
sc.tl.tsne(adata)
///data integrated
sc.external.pp.bbknn(adata, batch_key='orig.ident')

sc.tl.umap(adata)
adata
sc.pl.umap(adata, color=['orig.ident'])
showing the well integrated, picture below,
image
But,when i want to see the tsne picture, the batch from different sample showing up on the tsne but umap like above picture
,i runing ,
sc.tl.tsne(adata)
sc.pl.tsne(adata, color=['orig.ident'])
the picture show below, indicating that the integrated can not be worked on tsne.
image
So, why this tsne showing significantly different with the object just running over the integrated process.
any advice would be appreciated
Best,
hanhuihong

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reviewing the workflow entry points named in the report: sc.tl.tsne, sc.external.pp.bbknn, sc.tl.umap, and the corresponding plotting calls. Check the documentation and implementation for how each method obtains its input representation; done means establishing whether the reported difference is expected or identifying a reproducible defect with a focused example.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, 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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.