Markov screen plot functions and GRN regulon visualization - #78

Merged

WWXkenmo merged 70 commits into

theislab:mainfrom

emmaaer:markov_plot

Jul 17, 2026

Commits on Jul 6, 2026

Add Markov screen plotting functions
emmaaer
authored
f326b84
Add TF ranking and GRN visualization functions
emmaaer
authored
7a9617d
Add new plotting functions to API documentation
emmaaer
authored
8a16d37
Rename TFScreening to TFscreening_wrapper
emmaaer
authored
78e4aef
Refactor TFscreening function and enhance documentation
emmaaer
authored
18d2c2f
Add TFscreening_wrapper to tools documentation
emmaaer
authored
817674b

Commits on Jul 7, 2026

Refactor TFscreening with updated imports and tqdm
emmaaer
authored
ab09210
Add significance color mapping to _utils.py
emmaaer
authored
d17a25d
Refactor significance palette handling in _markov_screen
emmaaer
authored
6f029e7
Rename _driver_TF_ranking to _driver_TF_ranking.py
emmaaer
authored
6ad1d81
Add tqdm as a required dependency
emmaaer
authored
9adb8fc
Refactor significance-level color mapping import
emmaaer
authored
2084d89
Refactor TF ranking function and remove out_dir
emmaaer
authored
086c603

Commits on Jul 8, 2026

Refactor TF ranking plotting and update parameters
emmaaer
authored
d761a51
Refactor TF screening: remove SVG saving and update log
emmaaer
authored
808fff3
Remove SVG saving for Markov simulation plot
emmaaer
authored
ebbea5c
Add device parameter for GRN inference
emmaaer
authored
c6fe03d
Implement device fallback for model inference
emmaaer
authored
eb51375
Enhance device handling in GRN inference
emmaaer
authored
983588d
Remove duplicate plt.show() in _markov_screen.py
emmaaer
authored
ff2d464
Add device parameter to plotting function
emmaaer
authored
48d2156
Add new plotting functions to __init__.py
emmaaer
authored
8467aaa
Add TFscreening_wrapper to module exports
emmaaer
authored
bbbe29e

Commits on Jul 12, 2026

Commits on Jul 14, 2026

Fix Markov TF-screening pipeline and adopt rgv.tl/rgv.pl API consistently

WWXkenmo
and
claude
committed
1808bcf
Update test_markov.py
WWXkenmo
authored
79f8688

Commits on Jul 15, 2026

Separate function visits_diff_per_TF from markov_screen
emmaaer
authored
b717167
Add plots_visits_dist function to plotting tools
emmaaer
authored
211b0fd
Rename function to _plot_visits_dist_screen
emmaaer
authored
dd45b9b
Remove unused cellrank import
emmaaer
authored
a977426
Remove unused import of cellrank
emmaaer
authored
343f82f
Remove unused cellrank import
emmaaer
authored
f0003b1
Add missing return statements and remove automated file saving
emmaaer
committed
7ab5cb8
Separate plot_GRN_per_TF to new function
emmaaer
authored
cac7e06
Refactor GRN plotting functions and add matrix plot
emmaaer
authored
1c89a76
Refactor TFscreening to use regvelo plotting functions
emmaaer
authored
8b1bfcb
Refactor imports and update __all__ in __init__.py
emmaaer
authored
201d086
Rename function _plot_visits_dist to plot_visits_dist
emmaaer
authored
c016880
Rename function _plot_visits_dist_screen to plot_visits_dist_screen
emmaaer
authored
0238a58
Rename function _visits_diff_per_tf to visits_diff_per_tf
emmaaer
authored
2e084b0
Remove unused parameter from function definition
emmaaer
authored
e194e25
fix: comprehensive code review fixes for _TFscreening.py
emmaaer
committed
a3585cd
Remove matrixplot for TF hits in ranking script
emmaaer
authored
0f99023
Update plot title to include target type
emmaaer
authored
a446297
Create _plot_grn_weight.py for GRN weight plotting
emmaaer
authored
c197c9b
Remove plot_grn_weight function and update references
emmaaer
authored
87b5877
Refactor imports and __all__ in __init__.py
emmaaer
authored
f90a13d
fix: add coef parameter to plot_regulon function
emmaaer
committed
eb18ad5
Update _driver_TF_ranking.py
emmaaer
authored
3962868
Update _plot_grn_weight.py
emmaaer
authored
99b2572

Commits on Jul 16, 2026

Refactor Markov TF screening tool and plotting API

WWXkenmo
and
claude
committed
f98c51c
Update _compute_TF_regulon.py docstring
emmaaer
authored
ee21ae7
Update _plot_TF_regulon.py with TF-specific loading
emmaaer
authored
0af3e05
Update test_markov.py
emmaaer
authored
e495cae
Update test_markov.py with correct function call
emmaaer
authored
21c90e7
Update _compute_TF_regulon.py with correct printout
emmaaer
authored
6aada69
Update test_markov.py with device value
emmaaer
authored
0964d04
Update test_markov.py with parameter reordering
emmaaer
authored
f7968f1
Update test_markov.py

WWXkenmo
and
claude
committed
8aa3566
Added _plot_GRN_per_TF.py
emmaaer
authored
d731b6f
Update test_markov.py to single plot function for TF regulon
emmaaer
authored
2e6765b
Delete src/regvelo/plotting/_plot_TF_regulon.py
emmaaer
authored
766a2b1
Update and rename _plot_GRN_per_TF.py to _plot_TF_regulon.py
emmaaer
authored
ca52114
Update __init__.py
emmaaer
authored
d4473c2
Remove usused parameter and redundant function def
emmaaer
authored
28dcb53
Remove unused parameter in plot function
emmaaer
authored
b755127

Commits on Jul 17, 2026

Fix and clarify docstrings for Markov screening / regulon plots

WWXkenmo
and
claude
committed
f9caa1c