Feature/inflow score #221

AtheerAS · 2025-11-12T10:56:44Z

Add inflow module and tutorials (incl. plotting functions & global score function).

codecov-commenter · 2025-11-12T15:11:30Z

Codecov Report

❌ Patch coverage is 0% with 321 lines in your changes missing coverage. Please review.
✅ Project coverage is 82.01%. Comparing base (674bfb1) to head (546a47d).
⚠️ Report is 669 commits behind head on main.

Files with missing lines	Patch %	Lines
...g/_plot_spatial_inflow_score_single_interaction.py	0.00%	174 Missing ⚠️
src/liana/method/sc/_compute_global_score.py	0.00%	84 Missing ⚠️
src/liana/plotting/_plot_lr_heatmap.py	0.00%	63 Missing ⚠️

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@@             Coverage Diff             @@
##             main     #221       +/-   ##
===========================================
- Coverage   92.57%   82.01%   -10.57%     
===========================================
  Files          41       69       +28     
  Lines        1280     3192     +1912     
===========================================
+ Hits         1185     2618     +1433     
- Misses         95      574      +479

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dbdimitrov

Hi @AtheerAS,

Thanks, looks great overall. Left only minor comments.

Major points to discuss:

Unit tests for each new functions (I suggest starting with those; then changes to the rest would be easier)🙏 🙏 🙏 PS. I added tests for inflow, so that I can extend it to consider compositions.
Can we try to think of some global summaries to add to lrdata.var? For example, simply the average or sum; a cell-type frequency scaled average, and e.g. one that represents the mean / var ratio for each interaction;
compute_global_score - I'm not sure if this should be constrained to lrdata objects; I also moved it to li.mt.sp; also, compute_global_specificity - to be more ... specific :)
Would it make more sense to filter non-zero variance for ls rather than lrdata at the end?
plot_spatial_inflow_score_single_interaction - let's try to pick a shorter and broader name; not limited to lrdata. More generally, is there any way to simplify a bit, maybe not all optional parameters are needed; i'd have nightmares that a user encountered an issue with it 😄 - see minor comments :)
Would be cool to include a function for the gradient plot also :)
Inflow tutorial: Also, something is off with the logic where the resource is filtered. The order can also be improved a bit - e.g. show a simple interaction, and explain it how you did in the presentation (with each variable side-by-side), then go into permutations, complex plots by cell type, etc.

dbdimitrov · 2025-11-15T10:28:41Z

src/liana/plotting/_plot_spatial_inflow_score_single_interaction.py

+import warnings
+from typing import List, Tuple, Optional, Union
+
+def plot_spatial_inflow_score_single_interaction(


Lets try to think of a snappier name, this is a bit excessive :) I would also not limit it to inflow scores; you are plotting multiple features across cell types on a slide; spatial_features_by_obs or spatial_features_by_group

src/liana/plotting/_plot_spatial_inflow_score_single_interaction.py

src/liana/method/sp/_compute_global_specificity.py

src/liana/method/sp/_compute_global_score.py

src/liana/method/sp/_compute_global_specificity.py

src/liana/method/sp/_compute_global_score.py

src/liana/plotting/_plot_spatial_inflow_score_single_interaction.py

src/liana/method/sp/_compute_global_specificity.py

src/liana/method/sp/_compute_global_score.py

AtheerAS · 2025-12-01T15:41:12Z

src/liana/method/sp/_compute_global_specificity.py

+    # Build observed df
+    parts = [n.split(lr_sep) for n in full_names.tolist()]
+    df = pd.DataFrame(parts, columns=["source", "ligand", "receptor", "target"])
+    df["lr_mean"] = values


changing lr_mean to specificity_rank to be compatible with liana_res format and function name.

AtheerAS · 2025-12-01T15:42:29Z

src/liana/method/sp/_compute_global_specificity.py

+    """Helper for splitting complex names."""
+    toks = name.split(complex_sep)
+    if len(toks) > 1:
+        return toks[0], complex_sep.join(toks[1:])


Edited this so complex name includes primary L/R as well (it was not).

…tmap plot function

AtheerAS · 2025-12-02T14:29:10Z

src/liana/plotting/_heatmap.py

+            # This should technically not be hit if df_satisfy wasn't empty, but kept for robustness
+            raise ValueError(f"No interactions found for ligand_complex={ligand_complex}, receptor_complex={receptor_complex} after groupby-level filtering.")
+
+    heatmap_df = df.pivot(index="source", columns="target", values="specificity_rank")


Pass values key parameter

AtheerAS · 2025-12-02T14:38:23Z

src/liana/plotting/_spatial_inflow.py

+from liana._logging import _logg
+
+@d.dedent
+def spatial_inflow(


feature_by_group

src/liana/method/sp/_compute_global_specificity.py

dbdimitrov

Hey, @AtheerAS, I left a second round of comments now that I tested re-running things.

LMK if I can clarify anything 🙏

src/liana/method/sp/_compute_global_specificity.py

src/liana/method/sp/_inflow.py

dbdimitrov · 2025-12-03T08:10:01Z

src/liana/plotting/_heatmap.py

+
+
+# convert p-values to stars
+def p_to_star(p):


This did not work in the tutorial. Also, let's try to make more general - e.g. see heatmap with star in test_inflow.ipynb

Would also make sense to have this function passed as a parameter to the function - I guess this would fix it; also make it a '_annotate_fun' and pass it to a annotate_lambda parameter; which is broader, not just pval -> then the function would work for e.g. cell pair proximity also

src/liana/plotting/_heatmap.py

Atheer Alsayah added 2 commits November 12, 2025 11:41

Add inflow script and related tutorial

09047ca

Update inflow dirs

546a47d

Atheer Alsayah added 2 commits November 14, 2025 12:54

Update inflow score plots functions

e8e34ac

Update inflow plot functions

ef344cb

AtheerAS force-pushed the feature/inflow-score branch from 4f9d525 to ef344cb Compare November 14, 2025 12:09

Update pplot function

08efd6b

dbdimitrov requested changes Nov 15, 2025

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dbdimitrov and others added 12 commits November 15, 2025 13:26

fix ruff issues

b3d3819

add tests for inflow

fd81d1c

rename tut; pass obsm_key

35fb772

prelim mudata application

30d0231

update minor comments

3e788e5

add spatial weights

22b0456

move to correct folder..

93d6824

random tests

c8e0cef

Update global specificity function & inflow tutorial

918bda9

Update inflow-related functions

1347885

Update inflow-related plots functions

b3b7abf

Update functions

352dbbf

AtheerAS commented Dec 1, 2025

View reviewed changes

Atheer Alsayah added 4 commits December 1, 2025 16:46

Add unittest for heatmap, update global specificity function, and hea…

2ddcee8

…tmap plot function

Update spatial_inflow plot function

7c04f89

Add inflow_spatial unittest

6d64019

unittest for global_specificity

d997f26

AtheerAS commented Dec 2, 2025

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src/liana/plotting/_spatial_inflow.py Outdated

from liana._logging import _logg

@d.dedent

def spatial_inflow(

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feature_by_group

Atheer Alsayah added 2 commits December 2, 2025 19:26

Inflow updates

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Update inflow-related functions

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dbdimitrov reviewed Dec 3, 2025

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merge

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dbdimitrov added 2 commits December 3, 2025 07:51

merge spatial weights

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mask acc to filter

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dbdimitrov reviewed Dec 3, 2025

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dbdimitrov and others added 9 commits December 3, 2025 09:18

add comment

2ba87d9

Update inflow.var operations: gini

da11dd9

drop gini metrics

1aa0d40

Update global specificity function - omit loops

21257b8

del heatmap fun

bf4e27a

changes to global spec

21d889b

add unittest for global spec

998a5e8

update compute specificity

dce5cb5

Update inflow score notebook

dfcc59b

Feature/inflow score #221

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