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Add layout option to coda plot_boxplots (#718) #932

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Merged
Zethson merged 8 commits into from
Apr 2, 2026
+10 −2
Merged

Add layout option to coda plot_boxplots (#718) #932

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ba32e1d
Add layout option to coda plot_boxplots (#718)
emekaokoli19 Mar 10, 2026
9090603
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 10, 2026
3f32e2d
[pre-commit.ci] pre-commit autoupdate (#924)
pre-commit-ci[bot] Mar 9, 2026
cd56918
fix CI (#927)
Zethson Mar 9, 2026
6cf918d
[pre-commit.ci] pre-commit autoupdate (#928)
pre-commit-ci[bot] Mar 10, 2026
41155c6
fix CI (#931)
Zethson Mar 10, 2026
9c570e3
Merge branch 'main' into fix-plot_boxplots
Zethson Mar 12, 2026
eaa6b51
Move docstring
Zethson Apr 2, 2026
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12 changes: 10 additions & 2 deletions pertpy/tools/_coda/_base_coda.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1512,6 +1512,7 @@ def plot_boxplots( # pragma: no cover # noqa: D417
level_order: list[str] = None,
figsize: tuple[float, float] | None = None,
dpi: int | None = 100,
layout: Literal["long", "wide"] = "long",
return_fig: bool = False,
) -> Figure | None:
"""Grouped boxplot visualization.
Expand All @@ -1531,10 +1532,13 @@ def plot_boxplots( # pragma: no cover # noqa: D417
args_boxplot: Arguments passed to sns.boxplot.
args_swarmplot: Arguments passed to sns.swarmplot.
figsize: Figure size.
dpi: Dpi setting.
dpi: DPI setting.
palette: The seaborn color map (name) for the barplot.
show_legend: If True, adds a legend.
level_order: Custom ordering of bars on the x-axis.
layout: Controls subplot layout when `plot_facets=True`.
"long": uses floor(sqrt(K)) resulting in taller layout.
"wide": uses ceil(sqrt(K)) resulting in wider layout.
{common_plot_args}

Returns:
Expand All @@ -1559,6 +1563,8 @@ def plot_boxplots( # pragma: no cover # noqa: D417
data = data[modality_key]
if isinstance(palette, Colormap):
palette = list(palette(range(len(data.obs[feature_name].unique()))))
if layout not in {"long", "wide"}:
raise ValueError("layout must be either 'long' or 'wide'")

# y scale transformations
if y_scale == "relative":
Expand Down Expand Up @@ -1608,6 +1614,8 @@ def plot_boxplots( # pragma: no cover # noqa: D417

K = X.shape[1]

col_wrap = int(np.ceil(np.sqrt(K))) if layout == "wide" else int(np.floor(np.sqrt(K)))

if figsize is not None:
height = figsize[0]
aspect = np.round(figsize[1] / figsize[0], 2)
Expand All @@ -1619,7 +1627,7 @@ def plot_boxplots( # pragma: no cover # noqa: D417
plot_df,
col="Cell type",
sharey=False,
col_wrap=int(np.floor(np.sqrt(K))),
col_wrap=col_wrap,
height=height,
aspect=aspect,
)
Expand Down
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