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02 run azimuth before kweight #737

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merged 75 commits into from
Sep 2, 2024

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maud-p
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@maud-p maud-p commented Aug 29, 2024

Purpose/implementation Section

Please link to the GitHub issue that this pull request addresses.

Copying the PR#706 #706 to:

• roll back to what we had in f98da21? (i.e., before all the k.weight debugging, etc.)
• use system() instead of source() for download-and-create-fetal-kidney-ref.R in 00_run_workflow.R

#703

What is the goal of this pull request?

I write a RMarkdown script to

  1. download the data from the fetal kidney atlas
  2. process it and create an azimuth compatible reference,

This will be used in the module to perform label transfer from the human fetal kidney atlas to the Wilms tumor samples.

Briefly describe the general approach you took to achieve this goal.

I used a different approach than described in the issue #703 .
I figured out that I can download the human fetal kidney data from cellxgene as a rds object.
url = "https://datasets.cellxgene.cziscience.com/40ebb8e4-1a25-4a33-b8ff-02d1156e4e9b.rds"

Like this, I didn't need to create a conda/renv enrironment.
The dockerfile from this PR is the same as the dockerfile from the PR #704 .

Of note however, using your documentation, I have been able to build a conda/renv container that actually allow to run the scripts I did so far, in case we need it in the future :)

If known, do you anticipate filing additional pull requests to complete this analysis module?

Yes! The next one will be to implement the label transfer in the sample report.

Results

What is the name of your results bucket on S3?

here is the command I used to upload the result to the bucket:

scripts/sync-results.py cell-type-wilms-tumor-06 \
    --bucket researcher-008971640512-us-east-2 \

What types of results does your code produce (e.g., table, figure)?

The azimuth compatible reference in a format of 2 files:

  • ref.Rds
  • idx.annoy

When running the 00_fetal_reference_kidney.Rmd, these two files will be saved in the module folder/marker-genes.

What is your summary of the results?

We build a reference that is compatible with the azimuth label transfer.

Provide directions for reviewers

I have one issue, using the RMarkdown 00_fetal_reference_kidney.Rmd, we can only build the reference manually running each chunk, but it do not work when we want to knittr as html report.
I could isolate the problem to the AzimuthReference function, might be related to this issue: satijalab/azimuth#219

What are the software and computational requirements needed to be able to run the code in this PR?

  1. Run the docker container,
  2. open RStudio from http://localhost:8787/
  3. in the module folder open the 00_fetal_reference_kidney.Rmd and run chunk by chunk (do not knittr!!)

Are there particularly areas you'd like reviewers to have a close look at?

Is there anything that you want to discuss further?

Author checklists

Check all those that apply.
Note that you may find it easier to check off these items after the pull request is actually filed.

Analysis module and review

Reproducibility checklist

  • Code in this pull request has been added to the GitHub Action workflow that runs this module.
  • The dependencies required to run the code in this pull request have been added to the analysis module Dockerfile.
  • If applicable, the dependencies required to run the code in this pull request have been added to the analysis module conda environment.yml file.
  • If applicable, R package dependencies required to run the code in this pull request have been added to the analysis module renv.lock file.

maud-p and others added 30 commits August 9, 2024 14:36
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Uncomment workflow triggers, download relevant project, and run workflow
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
…terize_fetal_kidney_reference_Stewart.Rmd

Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
…transfer_fetal_kidney_reference_Stewart.Rmd

Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
…transfer_fetal_kidney_reference_Stewart.Rmd

Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
…terize_fetal_kidney_reference_Stewart.Rmd

Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
maud-p and others added 8 commits August 30, 2024 15:51
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
…fetal-kidney-ref.R

Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
…processing.Rmd

Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
…transfer_fetal_full_reference_Cao.Rmd

Co-authored-by: Jaclyn Taroni <19534205+jaclyn-taroni@users.noreply.github.com>
@maud-p
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maud-p commented Aug 30, 2024

Thank you very much @jaclyn-taroni ! I'll do the last changes on the Read.me file right now and run the analysis over the evening/night. If everything fine, I should commit the 40 reports by tomorrow morning :) (European time, Vienna).

Thank you so much, looking forward the next steps :D

@maud-p
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maud-p commented Aug 30, 2024

@jaclyn-taroni FYI, the extraneous RDS files for samples 168-178 in my results bucket should have been removed using --destructive-sync !

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Thanks for the updates, @maud-p! I am going to approve at this time 👍🏻

There are a couple things that will make future PRs easier until we figure out how to approach testing the Azimuth notebooks. I will make those changes here and then get this merged in! 🥳

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5afefe3 is just the HTML output of the notebooks after the change in 7e877ed, which passed CI: https://github.com/AlexsLemonade/OpenScPCA-analysis/actions/runs/10656117562/job/29534402700

Merging without the check on running the module.

@jaclyn-taroni jaclyn-taroni merged commit a5b48b0 into AlexsLemonade:main Sep 2, 2024
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maud-p commented Sep 2, 2024

Thank you so much @jaclyn-taroni ! It is great to see the merge in the main branch :) I'll create a new branch from here and continue with PR #704 ! Thanks!!

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2 participants