Skip to content
This repository has been archived by the owner on Apr 19, 2023. It is now read-only.

sample_id is neither included in the AnnData obs nor displayed in batch effect correction reports anymore #171

Closed
IrinaMate opened this issue Mar 16, 2020 · 10 comments · Fixed by vib-singlecell-nf/harmony#6 or #178
Closed

sample_id is neither included in the AnnData obs nor displayed in batch effect correction reports anymore #171

IrinaMate opened this issue Mar 16, 2020 · 10 comments · Fixed by vib-singlecell-nf/harmony#6 or #178
Assignees
@dweemx
Labels
bug Something isn't working

Comments

@IrinaMate
Copy link

sample_id was quite useful especially when integrating multiple samples
@dweemx
Copy link
Contributor

dweemx commented Mar 16, 2020 •
edited
Loading

Did you experienced this bug when running the pipelines with .h5ad as input data format ?

@IrinaMate
Copy link
Author

Indeed that's the case

@IrinaMate IrinaMate changed the title sample_id is not anymore included in the AnnData obs sample_id is not anymore included in the AnnData obs with .h5ad as input Mar 16, 2020
@dweemx
Copy link
Contributor

dweemx commented Mar 16, 2020

This should be fixed in the develop branch:

nextflow \
   -C test_h5ad_input.bbknn.config \
   run \
      -r develop vib-singlecell-nf/vsn-pipelines \
      -entry bbknn \
      -resume

@IrinaMate
Copy link
Author

ok I was actually running harmony 🤓 but I'll move to develop branch

@dweemx
Copy link
Contributor

dweemx commented Mar 16, 2020

Whatever the batch effect correction method you are using, it should be fixed if you use -r develop.
Let me know it this works for you ;)

@dweemx dweemx added the bug Something isn't working label Mar 16, 2020
@dweemx dweemx self-assigned this Mar 16, 2020
@IrinaMate
Copy link
Author

yes sample_id is back

@IrinaMate
Copy link
Author

now I noticed that is back in clustering report but not in Single-Cell Report: Harmony Batch Correction report

@dweemx
Copy link
Contributor

dweemx commented Mar 16, 2020

What do you mean by sample_id "is back" in ... but not in ... ?

@IrinaMate
Copy link
Author

image
image (1)

@dweemx dweemx changed the title sample_id is not anymore included in the AnnData obs with .h5ad as input sample_id is neither included in the AnnData obs nor displayed in batch effect correction reports anymore Mar 17, 2020
dweemx added a commit to vib-singlecell-nf/harmony that referenced this issue Mar 17, 2020
@dweemx
Fix vib-singlecell-nf/vsn-pipelines#171 for harmony pipeline
2009d11
dweemx added a commit to vib-singlecell-nf/scanpy that referenced this issue Mar 17, 2020
@dweemx
Align bbknn and mnncorrect reports to harmony batch effect correction…
943bb44 
… report vib-singlecell-nf/vsn-pipelines#171
@dweemx
Copy link
Contributor

dweemx commented Mar 17, 2020

This should be fixed in develop branch

@dweemx dweemx mentioned this issue Mar 17, 2020
Merged
This was referenced Mar 17, 2020
Merged
Merged
Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.
Assignees

@dweemx dweemx

Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

Develop vib-singlecell-nf/harmony
Develop vib-singlecell-nf/vsn-pipelines
2 participants
@dweemx @IrinaMate