Open
Conversation
method/Spatial-mgcn/Spatial-mgcn.yml
Outdated
| - torch_geometric==2.1.0 | ||
| - torch_sparse==0.6.15 | ||
| - torch_scatter==2.0.9 | ||
| - git+https://github.com/cs-wangbo/Spatial-MGCN@cf4412df6db6276e0c8a3f036ff0b1661adfdb35 |
Collaborator
There was a problem hiding this comment.
If it can be installed via pip why is the repo cloned during the run?
Contributor
Author
There was a problem hiding this comment.
It cannot be installed via pip. I updated the yml
method/Spatial-mgcn/Spatial-mgcn.py
Outdated
|
|
||
| # Normalize data: min_cells, calculate HVG and scale | ||
| sc.pp.filter_genes(adata, min_cells=100) | ||
| sc.pp.highly_variable_genes(adata, flavor="seurat_v3", n_top_genes=config["fdim"]) |
Collaborator
There was a problem hiding this comment.
Is there a reason not to use existing feature selection?
Contributor
Author
There was a problem hiding this comment.
I changed it to the existing feature selection now. But I left their feature selection as comments to make it easier to compare the performance of both ways.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
config/config_1.jsonwith hyperparameters for DLPFCCALC_ARItoTrueinSpatial-mgcn.py.CALC_ARI = True.