cellestial 0.48.2__tar.gz → 0.48.3__tar.gz

{cellestial-0.48.2 → cellestial-0.48.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellestial
-Version: 0.48.2
+Version: 0.48.3
 Summary: 
 License-Expression: Apache-2.0
 License-File: LICENSE

{cellestial-0.48.2 → cellestial-0.48.3}/cellestial/datasets/datasets.py

@@ -70,19 +70,21 @@ def _run_steps(
     """
     Drive a sequence of preprocessing steps with a tqdm progress bar.
 
-    Each step is a ``(label, code, action)`` triple. The bar description is set
-    to ``"{desc} | {label}: {code}"`` before ``action`` runs, so the user sees
-    both a human label and the underlying call. ``FutureWarning`` and
-    ``UserWarning`` are silenced for the duration so they don't clutter the bar;
-    the suppression is scoped to this call only.
-
     Parameters
     ----------
     steps : Sequence[tuple[str, str, Callable[[], object]]]
-        Steps to execute in order. ``label`` is human-readable, ``code`` is a
-        short representation of the call, ``action`` performs the work.
+        Steps to execute in order. `label` is human-readable, `code` is a
+        short representation of the call, `action` performs the work.
     desc : str
-        Prefix shown on every step's description, e.g. ``"Preprocessing pbmc3k"``.
+        Prefix shown on every step's description, e.g. `"Preprocessing pbmc3k"`.
+
+    Notes
+    -----
+    Each step is a `(label, code, action)` triple. The bar description is set
+    to `"{desc} | {label}: {code}"` before `action` runs, so the user sees
+    both a human label and the underlying call. `FutureWarning` and
+    `UserWarning` are silenced for the duration so they don't clutter the bar;
+    the suppression is scoped to this call only.
     """
     import contextlib
     import os
@@ -165,9 +167,6 @@ def pbmc3k(
     """
     Download and preprocess the pbmc3k dataset.
 
-    Adopted from
-    https://scanpy.readthedocs.io/en/stable/tutorials/basics/clustering.html.
-
     Parameters
     ----------
     cache_directory : str | Path | PathLike
@@ -184,6 +183,11 @@ def pbmc3k(
     -------
     AnnData
         The preprocessed pbmc3k dataset.
+
+    Notes
+    -----
+    Adopted from
+    https://scanpy.readthedocs.io/en/stable/tutorials/basics/clustering.html.
     """
     _require_extras("pbmc3k", "scanpy", "pooch")
 
@@ -426,15 +430,12 @@ def from_url(
     bring: bool = True,
 ) -> AnnData:
     """
-    Download an ``.h5ad`` dataset from a direct HTTP(S) URL.
-
-    Generic loader for any host that serves an AnnData ``.h5ad`` file at a
-    stable URL (CELLxGENE, Zenodo, Figshare, S3 buckets, etc.).
+    Download an `.h5ad` dataset from a direct HTTP(S) URL.
 
     Parameters
     ----------
     url : str
-        Direct URL to a downloadable ``.h5ad`` file.
+        Direct URL to a downloadable `.h5ad` file.
     name : str, optional
         Name for the cached file (without extension). If omitted, the cache
         filename is derived from the URL's last path segment.
@@ -459,6 +460,11 @@ def from_url(
         If `name` is not given and no filename can be derived from `url`.
     OSError
         If the downloaded file size does not match the expected size.
+
+    Notes
+    -----
+    Generic loader for any host that serves an AnnData `.h5ad` file at a
+    stable URL (CELLxGENE, Zenodo, Figshare, S3 buckets, etc.).
     """
     from urllib.parse import urlparse
     from urllib.request import urlopen
@@ -528,15 +534,12 @@ def from_cellxgene(
     """
     Download a dataset from CELLxGENE by URL or UUID.
 
-    Thin wrapper around `from_url` that accepts a CELLxGENE dataset UUID
-    directly and constructs the canonical download URL.
-
     Parameters
     ----------
     source : str
         A CELLxGENE dataset UUID (e.g.
-        ``7cdea341-ca7a-40fd-8192-b8ecb2d7b91e``) or a full ``.h5ad`` URL (e.g.
-        ``https://datasets.cellxgene.cziscience.com/<uuid>.h5ad``).
+        `7cdea341-ca7a-40fd-8192-b8ecb2d7b91e`) or a full `.h5ad` URL (e.g.
+        `https://datasets.cellxgene.cziscience.com/<uuid>.h5ad`).
     name : str, optional
         Name for the cached file (without extension). Defaults to the dataset
         UUID parsed from `source`.
@@ -561,6 +564,11 @@ def from_cellxgene(
         If `source` is neither a CELLxGENE dataset UUID nor a URL containing one.
     OSError
         If the downloaded file size does not match the expected size.
+
+    Notes
+    -----
+    Thin wrapper around `from_url` that accepts a CELLxGENE dataset UUID
+    directly and constructs the canonical download URL.
     """
     match = _UUID_PATTERN.search(source)
     if match is None:
@@ -594,8 +602,6 @@ def breast_cancer_atlas(
     """
     Download the breast cancer cell atlas from CELLxGENE.
 
-    Thin wrapper around `from_cellxgene` with the atlas UUID baked in.
-
     Parameters
     ----------
     cache_directory : str | Path | PathLike
@@ -617,6 +623,10 @@ def breast_cancer_atlas(
     ------
     OSError
         If the downloaded file size does not match the expected size.
+
+    Notes
+    -----
+    Thin wrapper around `from_cellxgene` with the atlas UUID baked in.
     """
     return from_cellxgene(
         "7cdea341-ca7a-40fd-8192-b8ecb2d7b91e",

{cellestial-0.48.2 → cellestial-0.48.3}/cellestial/layers/_deferred.py

@@ -14,25 +14,27 @@ class DeferredLayer(PlotSpec):
     """
     A layer whose construction depends on an existing plot's data and aesthetics.
 
-    Built by cellestial layer functions that need to introspect the plot they are
-    added to. Rather than taking the plot explicitly (``plot + cl.layer(plot)``),
-    the real layer is assembled at ``+`` time via :meth:`__radd__`, so callers
-    write ``plot + cl.layer()``.
-
-    Why subclass ``PlotSpec``? Python's reflected operator priority rule says
-    that when the right operand's class is a subclass of the left operand's
-    class, ``b.__radd__(a)`` is tried *before* ``a.__add__(b)``. Lets-Plot's
-    ``PlotSpec.__add__`` raises ``TypeError`` for unknown types instead of
-    returning ``NotImplemented``, so the usual ``__radd__`` fallback would
-    never fire, subclassing restores that fallback via the priority rule.
-    The base ``__init__`` is deliberately bypassed because ``DeferredLayer``
-    does not carry real plot data; only :meth:`__radd__` is ever used.
-
     Parameters
     ----------
     builder : Callable[[PlotSpec], LayerSpec | FeatureSpec | FeatureSpecArray]
         Callable that accepts the receiving plot and returns the concrete layer
         (or a feature array) to add to it.
+
+    Notes
+    -----
+    Built by cellestial layer functions that need to introspect the plot they are
+    added to. Rather than taking the plot explicitly (`plot + cl.layer(plot)`),
+    the real layer is assembled at `+` time via :meth:`__radd__`, so callers
+    write `plot + cl.layer()`.
+
+    Why subclass `PlotSpec`? Python's reflected operator priority rule says
+    that when the right operand's class is a subclass of the left operand's
+    class, `b.__radd__(a)` is tried *before* `a.__add__(b)`. Lets-Plot's
+    `PlotSpec.__add__` raises `TypeError` for unknown types instead of
+    returning `NotImplemented`, so the usual `__radd__` fallback would
+    never fire, subclassing restores that fallback via the priority rule.
+    The base `__init__` is deliberately bypassed because `DeferredLayer`
+    does not carry real plot data; only :meth:`__radd__` is ever used.
     """
 
     __slots__ = ("_builder",)

{cellestial-0.48.2 → cellestial-0.48.3}/cellestial/layers/arrow.py

@@ -148,8 +148,8 @@ def arrow_axis(
     ----------
     plot : PlotSpec | None, default=None
         If provided, the arrow axis is built from this plot's data and aesthetics
-        regardless of which plot the resulting layer is added to. When ``None``,
-        the layer is deferred and introspects the plot it is added to via ``+``.
+        regardless of which plot the resulting layer is added to. When `None`,
+        the layer is deferred and introspects the plot it is added to via `+`.
     size : float
         Size of the arrow.
     color : str

{cellestial-0.48.2 → cellestial-0.48.3}/cellestial/layers/bracket.py

@@ -278,21 +278,18 @@ def bracket(
     """
     Layer of `geom_bracket` annotating pairwise significance between groups.
 
-    Pairwise tests are computed from the plot's retrieved DataFrame using the `x`
-    aesthetic as the grouping column and the `y` aesthetic as the value column.
-
     Parameters
     ----------
     plot : PlotSpec | None, default=None
         If provided, brackets are computed from this plot's data and aesthetics
-        regardless of which plot the resulting layer is added to. When ``None``,
-        the layer is deferred and introspects the plot it is added to via ``+``.
+        regardless of which plot the resulting layer is added to. When `None`,
+        the layer is deferred and introspects the plot it is added to via `+`.
         Expected to be a distribution plot (e.g. `violin`, `boxplot`).
     comparisons : Sequence[Sequence[str]] | None, default=None
-        Specific group pairs to test, e.g. ``[("A", "B"), ("A", "C")]``.
+        Specific group pairs to test, e.g. `[("A", "B"), ("A", "C")]`.
         If None, every pair of groups present in the plot is compared.
-        ``"*"`` on either side expands to all other groups, so
-        ``[("A", "*")]`` compares ``A`` against every remaining group.
+        `"*"` on either side expands to all other groups, so
+        `[("A", "*")]` compares `A` against every remaining group.
     test : {'mannwhitney', 'ttest'}, default='mannwhitney'
         Statistical test used for each pairwise comparison.
         'mannwhitney' is non-parametric and recommended for expression data.
@@ -303,41 +300,41 @@ def bracket(
         Multiple-testing correction applied across the pairwise p-values.
     label : {'stars', 'pvalue', 'padj'} or sequence of those, default='stars'
         The bracket label to draw.
-        'stars' maps p-values to asterisks (``****`` < 0.0001, ``***`` < 0.001,
-        ``**`` < 0.01, ``*`` < 0.05, ``ns`` otherwise).
+        'stars' maps p-values to asterisks (`****` < 0.0001, `***` < 0.001,
+        `**` < 0.01, `*` < 0.05, `ns` otherwise).
         'pvalue' prints the raw p-value and 'padj' prints the adjusted p-value.
         A sequence merges each component with a newline, e.g.
-        ``label=("stars", "padj")`` stacks the stars on top of the adjusted p-value.
+        `label=("stars", "padj")` stacks the stars on top of the adjusted p-value.
     label_format : str, default='.3g'
         Format string used when `label` contains 'pvalue' or 'padj'.
     prefix : str, default=''
         Text prepended to the numeric p-value/padj labels. Ignored for the
         'stars' component. When `prefix_style` is '=' or '<', the symbol is
         inserted between `prefix` and the value with whitespace around it,
-        so ``prefix='p'`` with ``prefix_style='='`` renders ``'p = 0.001'``.
+        so `prefix='p'` with `prefix_style='='` renders `'p = 0.001'`.
         When `prefix_style` is None, `prefix` is used as-is, so the caller
         is responsible for including any symbol and spacing.
     prefix_style : {'=', '<'} or None, default='='
         How the numeric portion of the label is rendered.
-        '=' shows the actual p-value with ``' = '`` inserted after `prefix`.
+        '=' shows the actual p-value with `' = '` inserted after `prefix`.
         '<' replaces the p-value with the star-bracket threshold it falls
-        below, with ``' < '`` inserted after `prefix`, giving
-        ``'p < 0.0001'``, ``'p < 0.001'``, ``'p < 0.01'``, or ``'p < 0.05'``.
-        Non-significant comparisons render as ``'p > 0.05'``.
+        below, with `' < '` inserted after `prefix`, giving
+        `'p < 0.0001'`, `'p < 0.001'`, `'p < 0.01'`, or `'p < 0.05'`.
+        Non-significant comparisons render as `'p > 0.05'`.
         None disables symbol insertion; the caller supplies any symbol via
         `prefix`.
     separator : str, default=' '
         Separator used to join components when `label` is a sequence with
-        more than one entry (e.g. ``('stars', 'padj')``).
+        more than one entry (e.g. `('stars', 'padj')`).
     threshold : float | None, default=None
         If provided, only comparisons whose p-value (adjusted if `correction` is not
         'none') is below this threshold are drawn.
     y_position : float | None, default=None
         Vertical position of the lowest bracket. If None, it is placed above
-        the maximum `y` value with a gap of ``y_padding * y_range``.
+        the maximum `y` value with a gap of `y_padding * y_range`.
     y_step : float | None, default=None
         Vertical spacing between stacked brackets. If None, defaults to
-        ``y_padding * y_range``.
+        `y_padding * y_range`.
     y_padding : float, default=0.08
         Fraction of the `y` range used as vertical padding above the data
         and as the default spacing between stacked brackets.
@@ -377,6 +374,11 @@ def bracket(
         If a statistical option or label option is invalid, or there are too
         few observations to compute brackets.
 
+    Notes
+    -----
+    Pairwise tests are computed from the plot's retrieved DataFrame using the `x`
+    aesthetic as the grouping column and the `y` aesthetic as the value column.
+
     Examples
     --------
     Annotate a violin plot (or boxplot) with pairwise significance stars.
@@ -414,7 +416,7 @@ def bracket(
             y_padding=0.2,
         )
 
-    Use ``"*"`` to compare one group against every other.
+    Use `"*"` to compare one group against every other.
 
     .. jupyter-execute::
         :emphasize-lines: 2

{cellestial-0.48.2 → cellestial-0.48.3}/cellestial/layers/ondata_legend.py

@@ -52,8 +52,8 @@ def ondata_legend(
     ----------
     plot : PlotSpec | None, default=None
         If provided, labels are computed from this plot's data and aesthetics
-        regardless of which plot the resulting layer is added to. When ``None``,
-        the layer is deferred and introspects the plot it is added to via ``+``.
+        regardless of which plot the resulting layer is added to. When `None`,
+        the layer is deferred and introspects the plot it is added to via `+`.
     x : str | None, default=None
         The column name in the data used for x-axis coordinates. e.g 'X_UMAP1'.
         If None, it will be inferred from the plot aesthetics.

{cellestial-0.48.2 → cellestial-0.48.3}/cellestial/layers/outline.py

@@ -120,8 +120,8 @@ def cluster_outlines(
         E.g `groups=[['A', 'B']]` will outline groups A and B as if they were one cluster.
     plot : PlotSpec | None, default=None
         If provided, outlines are computed from this plot's data and aesthetics
-        regardless of which plot the resulting layer is added to. When ``None``,
-        the layer is deferred and introspects the plot it is added to via ``+``.
+        regardless of which plot the resulting layer is added to. When `None`,
+        the layer is deferred and introspects the plot it is added to via `+`.
     padding : float, default=1.5
         The spatial buffer added to the cluster's bounding box before calculating density.
         Increasing this value allows the density 'cloud' to expand further from the outermost

{cellestial-0.48.2 → cellestial-0.48.3}/cellestial/layers/stream.py

@@ -50,8 +50,8 @@ def stream(
     ----------
     plot : PlotSpec | None, default=None
         If provided, streams are computed from this plot's data and aesthetics
-        regardless of which plot the resulting layer is added to. When ``None``,
-        the layer is deferred and introspects the plot it is added to via ``+``.
+        regardless of which plot the resulting layer is added to. When `None`,
+        the layer is deferred and introspects the plot it is added to via `+`.
     color : str, default="#1f1f1f"
         Color of the stream lines.
     alpha : float, default=0.7
@@ -153,7 +153,7 @@ def stream(
 
     Stream as a separate layer to showcase the modularity of layers in Cellestial.
     Here the data source is passed explicitly because the receiving plot
-    (``ggplot()``) has no embedding to introspect.
+    (`ggplot()`) has no embedding to introspect.
 
     .. jupyter-execute::
 

{cellestial-0.48.2 → cellestial-0.48.3}/cellestial/single/basic/bar.py

@@ -97,7 +97,8 @@ def bar(
     if variable_keys is None:
         variable_keys = _select_variable_keys(data, keys)
     else:
-        list(variable_keys).extend(_select_variable_keys(data, keys))
+        variable_keys = list(variable_keys)
+        variable_keys.extend(_select_variable_keys(data, keys))
     axis = axis or _determine_axis(data=data, keys=keys)
     # BUILD: the bar plot
     br = baseplot(

{cellestial-0.48.2 → cellestial-0.48.3}/cellestial/single/basic/scatter.py

@@ -123,8 +123,8 @@ def scatter(
     if variable_keys is None:
         variable_keys = _select_variable_keys(data, keys)
     else:
-        list(variable_keys).extend(_select_variable_keys(data, keys))
-
+        variable_keys = list(variable_keys)
+        variable_keys.extend(_select_variable_keys(data, keys))
     axis = axis or _determine_axis(data=data, keys=keys)
     # BUILD: the scatter plot
     scttr = baseplot(

{cellestial-0.48.2 → cellestial-0.48.3}/cellestial/single/core/dimensional.py

@@ -102,34 +102,10 @@ def dimensional(
         The name to give to barcode (or index) column in the dataframe.
     color_low : str, default='#e6e6e6'
         The color to use for the low end of the color gradient.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
-        - Applies to continuous (non-categorical) data.
-
     color_mid : str, default=None
         The color to use for the middle part of the color gradient.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
-        - Applies to continuous (non-categorical) data.
-
     color_high : str, default='#377EB8'
         The color to use for the high end of the color gradient.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
-        - Applies to continuous (non-categorical) data.
-
     mid_point : {'mean', 'median', 'mid'} | float, default='median'
         The midpoint (in data value) of the color gradient.
         Can be 'mean', 'median' and 'mid' or a number (float or int).
@@ -145,14 +121,6 @@ def dimensional(
         Size of the arrow.
     arrow_color : str, default='#3f3f3f'
         Color of the arrows.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
-
-
     arrow_angle : float, default=10
         Angle of the arrow head in degrees.
     legend_ondata: bool, default=False

{cellestial-0.48.2 → cellestial-0.48.3}/cellestial/single/core/distribution.py

@@ -259,7 +259,7 @@ def violin(
         e.g., 'total_counts' or a gene name.
     group_by : str | None, default=None
         Column to group observations on the x-axis.
-        If not provided, falls back to ``fill``, ``color``, or the variable column.
+        If not provided, falls back to `fill`, `color`, or the variable column.
     mapping : FeatureSpec | None, default=None
         Additional aesthetic mappings for the plot, the result of `aes()`.
     axis : {0,1} | None, default=None
@@ -282,28 +282,10 @@ def violin(
         Use 'none' to disable tooltips.
     geom_fill : str | None, default=None
         Fill color for all violins in the violin plot.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
     geom_color : str | None, default=None
         Border color for all violins in the violin plot.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
     point_color : str, default='#1f1f1f'
         Color for the points in the violin plot.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
     point_alpha : float, default=0.7
         Alpha (transparency) for the points in the violin plot.
     point_size : float, default=0.5
@@ -501,7 +483,7 @@ def boxplot(
         e.g., 'total_counts' or a gene name.
     group_by : str | None, default=None
         Column to group observations on the x-axis.
-        If not provided, falls back to ``fill``, ``color``, or the variable column.
+        If not provided, falls back to `fill`, `color`, or the variable column.
     mapping : FeatureSpec | None, default=None
         Additional aesthetic mappings for the plot, the result of `aes()`.
     axis : {0,1} | None, default=None
@@ -524,28 +506,10 @@ def boxplot(
         Use 'none' to disable tooltips.
     geom_fill : str | None, default=None
         Fill color for all boxplots in the boxplot.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
     geom_color : str | None, default=None
         Border color for all boxplots in the boxplot.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
     point_color : str, default='#1f1f1f'
         Color for the points in the boxplot.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
     point_alpha : float, default=0.7
         Alpha (transparency) for the points in the boxplot.
     point_size : float, default=0.5

{cellestial-0.48.2 → cellestial-0.48.3}/cellestial/single/core/distributions.py

@@ -69,7 +69,7 @@ def violins(
         e.g., ['total_counts', 'pct_counts_in_top_50_genes'] or a list of gene names.
     group_by : str | None, default=None
         Column to group observations on the x-axis.
-        If not provided, falls back to ``fill``, ``color``, or the variable column.
+        If not provided, falls back to `fill`, `color`, or the variable column.
     mapping : FeatureSpec | None, default=None
         Additional aesthetic mappings for the plot, the result of `aes()`.
     axis : {0,1} | None, default=None
@@ -90,28 +90,10 @@ def violins(
         Use 'none' to disable tooltips.
     geom_fill : str | None, default=None
         Fill color for all violins in the violin plot.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
     geom_color : str | None, default=None
         Border color for all violins in the violin plot.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
     point_color : str, default='#1f1f1f'
         Color for the points in the violin plot.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
     point_alpha : float, default=0.7
         Alpha (transparency) for the points in the violin plot.
     point_size : float, default=0.5
@@ -326,7 +308,7 @@ def boxplots(
         e.g., ['total_counts', 'pct_counts_in_top_50_genes'] or a list of gene names.
     group_by : str | None, default=None
         Column to group observations on the x-axis.
-        If not provided, falls back to ``fill``, ``color``, or the variable column.
+        If not provided, falls back to `fill`, `color`, or the variable column.
     mapping : FeatureSpec | None, default=None
         Additional aesthetic mappings for the plot, the result of `aes()`.
     axis : {0,1} | None, default=None
@@ -347,28 +329,10 @@ def boxplots(
         Use 'none' to disable tooltips.
     geom_fill : str | None, default=None
         Fill color for all boxplots in the boxplot.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
     geom_color : str | None, default=None
         Border color for all boxplots in the boxplot.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
     point_color : str, default='#1f1f1f'
         Color for the points in the boxplot.
-
-            **Accepts:**
-
-            - hex code e.g. '#f1f1f1'
-            - color name (https://lets-plot.org/python/pages/named_colors.html).
-            - RGB/RGBA e.g. 'rgb(0, 0, 255)', 'rgba(0, 0, 255, 0.5)'.
     point_alpha : float, default=0.7
         Alpha (transparency) for the points in the boxplot.
     point_size : float, default=0.5