Per-point size array is cumulatively reordered across multi-color subplots

[Marius1311]

Per-point size array is cumulatively reordered across multi-color subplots

Bug description

When calling sc.pl.embedding (or sc.pl.umap, etc.) with multiple color keys and a per-point size array, the marker sizes are incorrect in all subplots after the first.

The root cause is in scatterplots.py (line 299): the size variable is reordered in-place within the per-color loop, but the reordered result carries over to the next iteration:

for count, (value_to_plot, dims) in enumerate(zip(color, dimensions, strict=True)):
    ...
    order = ...  # computed from this color's values
    if isinstance(size, np.ndarray):
        size = np.array(size)[order]  # mutates the loop variable!

Each subplot computes its own order for z-ordering, but applies it to the already-reordered size from the previous iteration. This means:

• Subplot 1: correct sizes
• Subplot 2: sizes scrambled by order_1 ∘ order_2
• Subplot 3: sizes scrambled by order_1 ∘ order_2 ∘ order_3
• etc.

Note that color_source_vector, color_vector, and coords don't have this problem because they are freshly computed from adata / basis_values each iteration.

Reproduction

import scanpy as sc
import numpy as np

adata = sc.datasets.pbmc3k_processed()
sizes = np.random.default_rng(0).uniform(10, 200, size=adata.n_obs)
sc.pl.umap(adata, color=["louvain", "n_genes", "n_counts"], size=sizes)
# Dot sizes visibly differ across the three panels despite being the same array

Expected behavior

The same per-point size array should be applied consistently to all subplots: the i-th point should always get size[i], regardless of what z-ordering is applied.

Suggested fix

Use a loop-local variable (e.g., _size) so each iteration reorders from the original array. See PR #4023.

Versions

Confirmed on main as of commit 1fbe008d.

[Ekin-Kahraman]

I'd like to work on this. The root cause looks like the size array being reordered in-place across loop iterations — I'll submit a PR with a copy fix.