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Warn and render na_color when color column is all-NaN #637

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Merged
timtreis merged 2 commits into from
Apr 24, 2026
+6 −6
Merged

Warn and render na_color when color column is all-NaN #637

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d192b79
Warn and render na_color when color column is all-NaN (#599)
timtreis Apr 24, 2026
560535b
Simplify all-NaN handling: always warn, never raise
timtreis Apr 24, 2026
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12 changes: 6 additions & 6 deletions src/spatialdata_plot/pl/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1102,14 +1102,14 @@ def _set_color_source_vec(

if color_series.isna().all():
element_label = _format_element_name(element_name)
location = f"table '{table_name}'" if table_name is not None else "the element"
dtype_hint = _build_alignment_dtype_hint(sdata, element, color_series, table_name)
raise ValueError(
f"Column '{value_to_plot}' for element '{element_label}' contains only missing values after aligning "
f"with {location}. This usually means the instance ids/indices could not be aligned or converted, so "
"colors cannot be determined. Please ensure the table annotates the element with matching instance ids."
f"{dtype_hint}"
hint_suffix = f" {dtype_hint.strip()}" if dtype_hint else ""
logger.warning(
f"Column '{value_to_plot}' for element '{element_label}' contains only NaN values; "
f"rendering with na_color.{hint_suffix}"
)
na_color_arr = np.full(len(color_series), na_color.get_hex_with_alpha())
return na_color_arr, na_color_arr, False

kind, processed = _infer_color_data_kind(
series=color_series,
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