Skip to content

Add example usage lymph node data and notebooks #326

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
fangliu117 wants to merge 3 commits into
base: dev
Choose a base branch
from
Open

Add example usage lymph node data and notebooks #326

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
0a41db9
Add example usage lymph node data and notebooks
fangliu117 Apr 14, 2025
6d88cc6
Refactor example usage notebook
fangliu117 Apr 15, 2025
9eb7da8
Updated example file with simplified output
fangliu117 Apr 15, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Binary file added examples/.DS_Store
View file
Open in desktop
Copy link
Contributor

@georgezakinih georgezakinih Apr 16, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@fangliu117, please remove this file.

Binary file not shown.
Binary file added examples/example_usage_lymphnode/Lymph_Node_Tissue.pickle
View file
Open in desktop
Copy link
Contributor

@georgezakinih georgezakinih Apr 16, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@fangliu117 , would you please put the h5ad instead of the pickle?

Binary file not shown.
1,823 changes: 1,823 additions & 0 deletions examples/example_usage_lymphnode/analysis.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

4,826 changes: 4,826 additions & 0 deletions examples/example_usage_lymphnode/example_lymphnode_data.csv
View file
Open in desktop

Large diffs are not rendered by default.

11 changes: 11 additions & 0 deletions examples/example_usage_lymphnode/phenograph_k60_1_to_renamed_clusters_relation_matrix.csv
View file
Open in desktop
Copy link
Contributor

@georgezakinih georgezakinih Apr 16, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@fangliu117, why this file is part of the commit?

Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
,target_ASMA+ cells,target_B cells,target_CD8 T cells,target_Follicular helper T cells (Tfh),target_Myeloid cells,target_NK cells,target_Proliferative B cells,target_Regulatory T cells,total
source_0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,100.0
source_1,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0,100.0
source_2,0.0,0.0,0.0,0.0,0.0,0.0,100.0,0.0,100.0
source_3,0.0,0.0,0.0,0.0,100.0,0.0,0.0,0.0,100.0
source_4,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0
source_5,0.0,0.0,100.0,0.0,0.0,0.0,0.0,0.0,100.0
source_6,0.0,0.0,0.0,100.0,0.0,0.0,0.0,0.0,100.0
source_7,100.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0
source_8,0.0,0.0,0.0,0.0,0.0,100.0,0.0,0.0,100.0
source_9,0.0,100.0,0.0,0.0,0.0,0.0,0.0,0.0,100.0
Binary file added examples/example_usage_lymphnode/sankey_diagram.png
View file
Open in desktop
Copy link
Contributor

@georgezakinih georgezakinih Apr 16, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@fangliu117, why this file is part of the commit?

Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.