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Cross-species Samosa
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samosa_fig1a.png
samosa_fig1a.png
1
1
samosa_fig1a.png
v2
Code
Execution Log
Messages
Environment
Review
Inputs
fig4_atlas_callouts.csv
fig4_atlas_centroids_m138ea.csv
Execution Log · v2
10:42:07.118INFOLoading environment · python 3.11.8, matplotlib 3.9.2
10:42:07.669INFOread_csv fig4_atlas_centroids_m138ea.csv → 5,672 rows
10:42:07.902INFOread_csv fig4_atlas_callouts.csv → 16 rows
10:42:08.331INFOapply_nature_style() · font.family = sans-serif
10:42:09.774WARN3 callout labels overlap in the “muscle” inset — nudging
10:42:11.205INFORendering 3 inset panels (i, ii, iii)
10:42:12.840DONESaved samosa_fig1a.png (2161×2244, 300 dpi) in 5.72s
Messages
S
You · 10:41
Rebuild Fig 1a as a single shared UMAP across all 138 species. Colour by cell-type family and box the three insets.
C
Claude · 10:42
Done — one embedding, 5,672 cell types coloured by family (neuron, muscle, immune, ciliated, germline, stem/progenitor). Added callout insets i–iii and a phylum palette. Rendered to samosa_fig1a.png.
S
You · 10:44
The family labels on the scatter are hard to read against the dense points. Can you add a white halo?
Environment
python3.11.8
matplotlib3.9.2
pandas2.2.2
numpy1.26.4
scanpy1.10.1
umap-learn0.5.6
Review checklist
Single shared embedding across all 138 species
Colour mapping matches HERO family palette
Inset boxes i–iii aligned to centroid callouts
Legend order & phylum palette (PHYL_PAL2) verified
Approved — 4 of 4 checks passing. Ready to place in the manuscript.