Fix some plot warnings (scverse#2844)

docs/release-notes/1.10.0.md

@@ -29,6 +29,7 @@
 * Fix testing package build {pr}`2468` {smaller}`P Angerer`
 * Fix setting `sc.settings.verbosity` in some cases {pr}`2605` {smaller}`P Angerer`
 * Fix all remaining pandas warnings {pr}`2789` {smaller}`P Angerer`
+* Fix some annoying plotting warnings around violin plots {pr}`2844` {smaller}`P Angerer`
 
 ```{rubric} Ecosystem
 ```

pyproject.toml

@@ -184,6 +184,10 @@ filterwarnings = [
     "error:The provided callable.* is currently using:FutureWarning",
     "error:The behavior of DataFrame concatenation with empty or all-NA entries is deprecated:FutureWarning",
     "error:A value is trying to be set on a copy of a slice from a DataFrame",
+    "error:No data for colormapping provided via 'c'",
+    "error:\\n*The `scale` parameter has been renamed and will be removed",
+    "error:\\n*Passing `palette` without assigning `hue` is deprecated",
+    "error:\\n*Setting a gradient palette using color= is deprecated",
 ]
 
 [tool.coverage.run]

scanpy/plotting/_anndata.py

@@ -838,6 +838,7 @@ def violin(
                     f"but is of dtype {adata.obs[groupby].dtype}."
                 )
             _utils.add_colors_for_categorical_sample_annotation(adata, groupby)
+            kwds["hue"] = groupby
             kwds["palette"] = dict(
                 zip(obs_df[groupby].cat.categories, adata.uns[f"{groupby}_colors"])
             )
@@ -909,7 +910,7 @@ def violin(
                 data=obs_tidy,
                 order=order,
                 orient="vertical",
-                scale=scale,
+                density_norm=scale,
                 ax=ax,
                 **kwds,
             )

scanpy/plotting/_dotplot.py

@@ -586,9 +586,7 @@ def _mainplot(self, ax):
         if self.are_axes_swapped:
             _size_df = _size_df.T
             _color_df = _color_df.T
-        self.cmap = self.kwds.get("cmap", self.cmap)
-        if "cmap" in self.kwds:
-            del self.kwds["cmap"]
+        self.cmap = self.kwds.pop("cmap", self.cmap)
 
         normalize, dot_min, dot_max = self._dotplot(
             _size_df,
@@ -627,7 +625,7 @@ def _dotplot(
         y_label: str | None = None,
         dot_max: float | None = None,
         dot_min: float | None = None,
-        standard_scale: Literal["var", "group"] = None,
+        standard_scale: Literal["var", "group"] | None = None,
         smallest_dot: float | None = 0.0,
         largest_dot: float | None = 200,
         size_exponent: float | None = 2,
@@ -737,9 +735,7 @@ def _dotplot(
         x = x.flatten() + 0.5
         frac = dot_size.values.flatten()
         mean_flat = dot_color.values.flatten()
-        cmap = plt.get_cmap(kwds.get("cmap", cmap))
-        if "cmap" in kwds:
-            del kwds["cmap"]
+        cmap = plt.get_cmap(cmap)
         if dot_max is None:
             dot_max = np.ceil(max(frac) * 10) / 10
         else:
@@ -786,11 +782,9 @@ def _dotplot(
             kwds = fix_kwds(
                 kwds,
                 s=size,
-                cmap=cmap,
                 linewidth=edge_lw,
                 facecolor="none",
                 edgecolor=edge_color,
-                norm=normalize,
             )
             dot_ax.scatter(x, y, **kwds)
         else:
@@ -801,11 +795,9 @@ def _dotplot(
             kwds = fix_kwds(
                 kwds,
                 s=size,
-                cmap=cmap,
                 color=color,
                 linewidth=edge_lw,
                 edgecolor=edge_color,
-                norm=normalize,
             )
 
             dot_ax.scatter(x, y, **kwds)

scanpy/plotting/_stacked_violin.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import warnings
 from typing import TYPE_CHECKING, Literal
 
 import numpy as np
@@ -13,7 +14,13 @@
 from .._utils import _doc_params
 from ._baseplot_class import BasePlot, _VarNames, doc_common_groupby_plot_args
 from ._docs import doc_common_plot_args, doc_show_save_ax, doc_vboundnorm
-from ._utils import _AxesSubplot, check_colornorm, make_grid_spec, savefig_or_show
+from ._utils import (
+    _AxesSubplot,
+    _deprecated_scale,
+    check_colornorm,
+    make_grid_spec,
+    savefig_or_show,
+)
 
 if TYPE_CHECKING:
     from collections.abc import (
@@ -52,7 +59,7 @@ class StackedViolin(BasePlot):
         Order in which to show the categories. Note: if `dendrogram=True`
         the categories order will be given by the dendrogram and `order`
         will be ignored.
-    scale
+    density_norm
         The method used to scale the width of each violin.
         If 'width' (the default), each violin will have the same width.
         If 'area', each violin will have the same area.
@@ -108,7 +115,7 @@ class StackedViolin(BasePlot):
     DEFAULT_JITTER_SIZE = 1
     DEFAULT_LINE_WIDTH = 0.2
     DEFAULT_ROW_PALETTE = None
-    DEFAULT_SCALE = "width"
+    DEFAULT_DENSITY_NORM: Literal["area", "count", "width"] = "width"
     DEFAULT_PLOT_YTICKLABELS = False
     DEFAULT_YLIM = None
     DEFAULT_PLOT_X_PADDING = 0.5  # a unit is the distance between two x-axis ticks
@@ -131,6 +138,18 @@ class StackedViolin(BasePlot):
     # None will draw unadorned violins.
     DEFAULT_INNER = None
 
+    def __getattribute__(self, name: str) -> object:
+        """Called unconditionally when accessing an instance attribute"""
+        # If the user has set the deprecated version on the class,
+        # and our code accesses the new version from the instance,
+        # return the user-specified version instead and warn.
+        # This is done because class properties are hard to do.
+        if name == "DEFAULT_DENSITY_NORM" and hasattr(self, "DEFAULT_SCALE"):
+            msg = "Don’t set DEFAULT_SCALE, use DEFAULT_DENSITY_NORM instead"
+            warnings.warn(msg, FutureWarning)
+            return object.__getattribute__(self, "DEFAULT_SCALE")
+        return object.__getattribute__(self, name)
+
     @old_positionals(
         "use_raw",
         "log",
@@ -224,7 +243,7 @@ def __init__(
         self.kwds.setdefault("cut", self.DEFAULT_CUT)
         self.kwds.setdefault("inner", self.DEFAULT_INNER)
         self.kwds.setdefault("linewidth", self.DEFAULT_LINE_WIDTH)
-        self.kwds.setdefault("scale", self.DEFAULT_SCALE)
+        self.kwds.setdefault("density_norm", self.DEFAULT_DENSITY_NORM)
 
     @old_positionals(
         "cmap",
@@ -233,7 +252,7 @@ def __init__(
         "jitter_size",
         "linewidth",
         "row_palette",
-        "scale",
+        "density_norm",
         "yticklabels",
         "ylim",
         "x_padding",
@@ -248,11 +267,13 @@ def style(
         jitter_size: int | None = DEFAULT_JITTER_SIZE,
         linewidth: float | None = DEFAULT_LINE_WIDTH,
         row_palette: str | None = DEFAULT_ROW_PALETTE,
-        scale: Literal["area", "count", "width"] | None = DEFAULT_SCALE,
+        density_norm: Literal["area", "count", "width"] = DEFAULT_DENSITY_NORM,
         yticklabels: bool | None = DEFAULT_PLOT_YTICKLABELS,
         ylim: tuple[float, float] | None = DEFAULT_YLIM,
         x_padding: float | None = DEFAULT_PLOT_X_PADDING,
         y_padding: float | None = DEFAULT_PLOT_Y_PADDING,
+        # deprecated
+        scale: Literal["area", "count", "width"] | None = None,
     ):
         r"""\
         Modifies plot visual parameters
@@ -277,7 +298,7 @@ def style(
             (see :func:`~seaborn.color_palette`).
             Alternatively, a single color name or hex value can be passed,
             e.g. `'red'` or `'#cc33ff'`.
-        scale
+        density_norm
             The method used to scale the width of each violin.
             If 'width' (the default), each violin will have the same width.
             If 'area', each violin will have the same area.
@@ -338,8 +359,14 @@ def style(
             self.plot_y_padding = y_padding
         if linewidth != self.kwds["linewidth"] and linewidth != self.DEFAULT_LINE_WIDTH:
             self.kwds["linewidth"] = linewidth
-        if scale != self.kwds["scale"] and scale != self.DEFAULT_SCALE:
-            self.kwds["scale"] = scale
+        density_norm = _deprecated_scale(
+            density_norm, scale, default=self.DEFAULT_DENSITY_NORM
+        )
+        if (
+            density_norm != self.kwds["density_norm"]
+            and density_norm != self.DEFAULT_DENSITY_NORM
+        ):
+            self.kwds["density_norm"] = density_norm
 
         return self
 
@@ -367,9 +394,7 @@ def _mainplot(self, ax):
         if self.are_axes_swapped:
             _color_df = _color_df.T
 
-        cmap = plt.get_cmap(self.kwds.get("cmap", self.cmap))
-        if "cmap" in self.kwds:
-            del self.kwds["cmap"]
+        cmap = plt.get_cmap(self.kwds.pop("cmap", self.cmap))
         normalize = check_colornorm(
             self.vboundnorm.vmin,
             self.vboundnorm.vmax,
@@ -418,9 +443,7 @@ def _make_rows_of_violinplots(
     ):
         import seaborn as sns  # Slow import, only import if called
 
-        row_palette = self.kwds.get("color", self.row_palette)
-        if "color" in self.kwds:
-            del self.kwds["color"]
+        row_palette = self.kwds.pop("color", self.row_palette)
         if row_palette is not None:
             if is_color_like(row_palette):
                 row_colors = [row_palette] * _color_df.shape[0]
@@ -484,10 +507,9 @@ def _make_rows_of_violinplots(
             row_ax = fig.add_subplot(gs[idx + 1, 1:-1])
             axs_list.append(row_ax)
 
-            if row_colors[idx] is None:
-                palette_colors = colormap_array[idx, :]
-            else:
-                palette_colors = None
+            palette_colors = (
+                list(colormap_array[idx, :]) if row_colors[idx] is None else None
+            )
 
             if not self.are_axes_swapped:
                 x = "genes"
@@ -506,6 +528,9 @@ def _make_rows_of_violinplots(
                 data=_df,
                 orient="vertical",
                 ax=row_ax,
+                # use a single `color`` if row_colors[idx] is defined
+                # else use the palette
+                hue=None if palette_colors is None else x,
                 palette=palette_colors,
                 color=row_colors[idx],
                 **self.kwds,
@@ -630,7 +655,7 @@ def stacked_violin(
     stripplot: bool = StackedViolin.DEFAULT_STRIPPLOT,
     jitter: float | bool = StackedViolin.DEFAULT_JITTER,
     size: int = StackedViolin.DEFAULT_JITTER_SIZE,
-    scale: Literal["area", "count", "width"] = StackedViolin.DEFAULT_SCALE,
+    scale: Literal["area", "count", "width"] = StackedViolin.DEFAULT_DENSITY_NORM,
     yticklabels: bool | None = StackedViolin.DEFAULT_PLOT_YTICKLABELS,
     order: Sequence[str] | None = None,
     swap_axes: bool = False,
@@ -779,7 +804,7 @@ def stacked_violin(
         jitter=jitter,
         jitter_size=size,
         row_palette=row_palette,
-        scale=kwds.get("scale", scale),
+        density_norm=kwds.get("density_norm", scale),
         yticklabels=yticklabels,
         linewidth=kwds.get("linewidth", StackedViolin.DEFAULT_LINE_WIDTH),
     ).legend(title=colorbar_title)

scanpy/plotting/_tools/__init__.py

@@ -27,6 +27,7 @@
     doc_vbound_percentile,
 )
 from .._utils import (
+    _deprecated_scale,
     savefig_or_show,
     timeseries,
     timeseries_as_heatmap,
@@ -1176,7 +1177,7 @@ def rank_genes_groups_matrixplot(
     "use_raw",
     "key",
     "split",
-    "scale",
+    "density_norm",
     "strip",
     "jitter",
     "size",
@@ -1195,13 +1196,15 @@ def rank_genes_groups_violin(
     use_raw: bool | None = None,
     key: str | None = None,
     split: bool = True,
-    scale: str = "width",
+    density_norm: Literal["area", "count", "width"] = "width",
     strip: bool = True,
     jitter: int | float | bool = True,
     size: int = 1,
     ax: Axes | None = None,
     show: bool | None = None,
     save: bool | None = None,
+    # deprecated
+    scale: Literal["area", "count", "width"] | None = None,
 ):
     """\
     Plot ranking of genes for all tested comparisons.
@@ -1225,7 +1228,7 @@ def rank_genes_groups_violin(
         was used in :func:`~scanpy.tl.rank_genes_groups`.
     split
         Whether to split the violins or not.
-    scale
+    density_norm
         See :func:`~seaborn.violinplot`.
     strip
         Show a strip plot on top of the violin plot.
@@ -1244,6 +1247,8 @@ def rank_genes_groups_violin(
     groups_names = adata.uns[key]["names"].dtype.names if groups is None else groups
     if isinstance(groups_names, str):
         groups_names = [groups_names]
+    density_norm = _deprecated_scale(density_norm, scale, default="width")
+    del scale
     axs = []
     for group_name in groups_names:
         if gene_names is None:
@@ -1274,7 +1279,7 @@ def rank_genes_groups_violin(
             hue_order=hue_order,
             hue="hue",
             split=split,
-            scale=scale,
+            density_norm=density_norm,
             orient="vertical",
             ax=ax,
         )
@@ -1287,7 +1292,7 @@ def rank_genes_groups_violin(
                 dodge=True,
                 hue_order=hue_order,
                 jitter=jitter,
-                color="black",
+                palette="dark:black",
                 size=size,
                 ax=_ax,
             )