Comseg cli - Githubissues

gustaveroussy / sopa

Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells

https://gustaveroussy.github.io/sopa/

BSD 3-Clause "New" or "Revised" License

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Comseg cli #76

Open tdefa opened 3 weeks ago

tdefa commented 3 weeks ago

implementation of ComSeg cli

An example to run comseg in CLI is in sopa/docs/tutorials/cli_other_segmentation.md
documentation at "sopa/docs/cli.md" was update fro comseg

A function transcript_segmentation() was created to handle both Baysor and ComSeg

quentinblampey commented 3 weeks ago

Here is a todo list for the next steps:

[ ] Update the Snakefile and utils.py
[ ] Have a complete ComSeg tutorial for API + CLI + snakemake
[ ] Have a ComSeg config for the toy dataset (used in the above snakemake tutorial)
[ ] Have a ComSeg config for a few major technologies (e.g., MERSCOPE and Xenium)

quentinblampey commented 3 weeks ago

Thanks for the changes! Regarding the CI, you can install pre-commit locally to fix the issues:

pre-commit install

pre-commit run --all-files

tdefa commented 3 weeks ago

Thanks for the changes! Regarding the CI, you can install pre-commit locally to fix the issues:
pre-commit install

pre-commit run --all-files

Ok thanks I just saw it

tdefa commented 3 weeks ago

I added comseg to the snakemake pipeline + few config file examples.

Now I will complete ComSeg tutorial for API + CLI + snakemake all in the file : "other_segmentations.ipynb" do you agree ?

quentinblampey commented 2 weeks ago

Thanks for your updates, it looks very good!

I fixed and cleaned a few things

Also, I had some issues running comseg, now I get an error 'PCA' object has no attribute 'explained_variance_' when running the patch step of comseg, do you know why? Two other things:

Installing comseg is not enough to have all the dependencies, I also needed to install alphashape / igraph / leidenalg. Do you think these could be added as a dependency of ComSeg for convenience?
I moved the tutorial in docs/tutorial/comseg.ipynb, can you check and fill the "Snakemake" and "CLI" sections? It can be pretty short, since it is very similar to the existing tutorial. For instance, for the Snakemake pipeline, you can provide the command line to run the toy dataset, and for the CLI you can do something similar to the CLI tutorial with Baysor.
Why do you need to do importlib.reload(method)?

After this, I will merge the PR!

tdefa commented 2 weeks ago

Ok thanks for reviewing!

PCA' object has no attribute 'explained_variance_' I will look at it and also complete dependency of ComSeg
forimportlib.reload(method) I will remove it I think it is a mistake

I will do additional tests on other data this week, before the next push.