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enh: Use radius for dotplot Bokeh#34

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hoxbro merged 7 commits into
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add_radius
Jun 25, 2025
Merged

enh: Use radius for dotplot Bokeh#34
hoxbro merged 7 commits into
mainfrom
add_radius

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@hoxbro

@hoxbro hoxbro commented May 28, 2025

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Add radius, which is currently being worked on in holoviz/holoviews#6599

closes #27

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codecov Bot commented May 28, 2025

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Codecov Report

❌ Patch coverage is 75.00000% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 80.20%. Comparing base (d3655c3) to head (4ed77b1).
⚠️ Report is 50 commits behind head on main.

Files with missing lines Patch % Lines
src/hv_anndata/plotting.py 75.00% 1 Missing and 1 partial ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #34      +/-   ##
==========================================
- Coverage   80.38%   80.20%   -0.18%     
==========================================
  Files           8        8              
  Lines         571      576       +5     
  Branches       60       61       +1     
==========================================
+ Hits          459      462       +3     
- Misses         82       83       +1     
- Partials       30       31       +1     

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@hoxbro
hoxbro marked this pull request as ready for review June 24, 2025 16:38
Comment thread src/hv_anndata/plotting.py Outdated
@hoxbro

hoxbro commented Jun 24, 2025

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@droumis can you give this a go? Remember to use the latest dev release of HoloViews.

@hoxbro
hoxbro requested a review from droumis June 24, 2025 17:09
@droumis

droumis commented Jun 25, 2025

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LGTM!

Code
import scanpy as sc
import holoviews as hv
from hv_anndata import Dotmap
import panel as pn

hv.extension("bokeh")
pn.extension()

adata = sc.datasets.pbmc68k_reduced()
sel_marker_genes = {
    "CD14+ Mono": ['FCN1'],
    "CD16+ Mono": ['FCGR3A'],
    "ID2-hi myeloid prog": ['ID2', 'S100A9'],
    "cDC2": ['CST3', 'LYZ', 'CLEC10A', 'FCER1A'],
    "Lymph prog": ['CD79B', 'IGLL1'],
    "B1 B": ['MS4A1', 'BLK'],
    "Plasma cells": ['MZB1'],
    "CD4+ T activated": ['CD4', 'IL7R'],
    "pDC": ['GZMB'],
}
dm = pn.panel(Dotmap(adata=adata, marker_genes=sel_marker_genes, groupby="bulk_labels").opts(responsive=True))
dm.servable()
GMT20250625-131809_Clip_Demetris.Roumis.s.Clip.06_25_2025.mp4

@droumis

droumis commented Jun 25, 2025

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feel free to merge

@hoxbro
hoxbro merged commit 66e6484 into main Jun 25, 2025
3 of 6 checks passed
@hoxbro
hoxbro deleted the add_radius branch June 25, 2025 13:24
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Dot size scaling for DotMap plot

2 participants