cellestial 0.58.2__tar.gz → 0.59.0__tar.gz

{cellestial-0.58.2 → cellestial-0.59.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellestial
-Version: 0.58.2
+Version: 0.59.0
 Summary: Interactive single-cell and spatial omics visualization library
 License-Expression: Apache-2.0
 License-File: LICENSE

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/complex/annotated_heatmap.py

@@ -359,7 +359,7 @@ def annotated_heatmap(
     color_low: str = "#0000ff",
     color_mid: str = "#ffffff",
     color_high: str = "#ff0000",
-    mid_point: Literal["mean", "median", "mid"] | float = "mid",
+    midpoint: Literal["mean", "median", "mid"] | float = "mid",
     max_rows: int | None = 1000,
     value_column: str = "value",
     variable_column: str = "variable",
@@ -446,7 +446,7 @@ def annotated_heatmap(
         Color for mid values in the heatmap gradient.
     color_high : str, default='#ff0000'
         Color for high values in the heatmap gradient.
-    mid_point : {'mean', 'median', 'mid'} | float, default='mid'
+    midpoint : {'mean', 'median', 'mid'} | float, default='mid'
         Midpoint for the heatmap color gradient.
     max_rows : int | None, default=1000
         Cap the number of plotted rows by averaging contiguous observations
@@ -495,7 +495,7 @@ def annotated_heatmap(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
         markers = ["C1QA", "PSAP", "CD79A", "CD79B", "CST3", "LYZ"]
 
         cl.annotated_heatmap(
@@ -608,7 +608,7 @@ def annotated_heatmap(
             color_low=color_low,
             color_mid=color_mid,
             color_high=color_high,
-            mid_point=mid_point,
+            midpoint=midpoint,
         )
         + key_scale
         + observation_scale

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/frames/__init__.py

@@ -4,11 +4,12 @@ from cellestial.frames.build import (
     anndata_variables_frame,
     build_frame,
 )
-from cellestial.frames.operations import _highest_expressed_genes_frame, _pca_variance_frame
+from cellestial.frames.operations import (  # noqa: F401
+    _highest_expressed_genes_frame,
+    _pca_variance_frame,
+)
 
 __all__ = [
-    "_highest_expressed_genes_frame",
-    "_pca_variance_frame",
     "anndata_observations_frame",
     "anndata_variable_columns",
     "anndata_variables_frame",

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/frames/build.py

@@ -350,7 +350,7 @@ def build_frame(
         import cellestial as cl
         import scanpy as sc
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
         frame = cl.build_frame(data, axis=0, include_dimensions=2)
         frame.head()
 
@@ -362,7 +362,7 @@ def build_frame(
         import cellestial as cl
         import scanpy as sc
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
         frame = cl.build_frame(data, variable_keys=["CD14", "HBA1"], include_dimensions=2)
         frame.head()
 

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/layers/__init__.py

@@ -1,5 +1,5 @@
 from cellestial.layers._deferred import DeferredLayer
-from cellestial.layers.arrow import _modify_axis, arrow_axis
+from cellestial.layers.arrow import _modify_axis, arrow_axis  # noqa: F401
 from cellestial.layers.bracket import bracket
 from cellestial.layers.ondata_legend import ondata_legend
 from cellestial.layers.outline import cluster_outlines
@@ -8,7 +8,6 @@ from cellestial.layers.utilities import borders
 
 __all__ = [
     "DeferredLayer",
-    "_modify_axis",
     "arrow_axis",
     "borders",
     "bracket",

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/layers/arrow.py

@@ -273,7 +273,7 @@ def arrow_axis(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         umap = cl.umap(data,"HBA2")
         umap
@@ -287,7 +287,7 @@ def arrow_axis(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         umap = cl.umap(data,"HBA2")
         umap + cl.arrow_axis()
@@ -301,7 +301,7 @@ def arrow_axis(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         umap = cl.umap(data,"HBA2")
         umap + cl.arrow_axis(length=0.20,color="dark_violet")

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/layers/bracket.py

@@ -401,7 +401,7 @@ def bracket(
 
         from lets_plot import *
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         violin = cl.violin(
             data,

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/layers/ondata_legend.py

@@ -121,7 +121,7 @@ def ondata_legend(
 
         from lets_plot import *
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         umap = cl.umap(data, key="cell_type_lvl1", axis_type="arrow", size=1.5)
         umap

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/layers/outline.py

@@ -192,7 +192,7 @@ def cluster_outlines(
 
         from lets_plot import *
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         umap = (
             cl.umap(data, key="cell_type_lvl1", axis_type="arrow", size=0.5, legend_ondata=True)
@@ -209,7 +209,7 @@ def cluster_outlines(
 
         from lets_plot import *
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         umap = (
             cl.umap(data, key="cell_type_lvl1", axis_type="arrow", size=0.5, legend_ondata=True)
@@ -226,7 +226,7 @@ def cluster_outlines(
 
         from lets_plot import *
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         umap = (
             cl.umap(data, key="cell_type_lvl1", axis_type="arrow", size=0.5, legend_ondata=True)

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/layers/stream.py

@@ -138,7 +138,7 @@ def stream(
 
         import cellestial as cl
 
-        data = cl.datasets.pancreas(cache_directory="data")
+        data = cl.datasets.pancreas()
 
         plot = cl.umap(
             data,
@@ -162,7 +162,7 @@ def stream(
 
         import cellestial as cl
 
-        data = cl.datasets.pancreas(cache_directory="data")
+        data = cl.datasets.pancreas()
 
         plot = cl.umap(
             data,

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/single/base/base.py

@@ -65,7 +65,7 @@ def plot(
         import cellestial as cl
         import scanpy as sc
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         p1 = (
             cl.plot(data, aes(x='cell_type_lvl1', y='n_genes'))
@@ -80,7 +80,7 @@ def plot(
         import cellestial as cl
         import scanpy as sc
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         p2 = (
             cl.plot(data, aes(x='cell_type_lvl1', y='n_genes'))

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/single/basic/bar.py

@@ -67,7 +67,7 @@ def bar(
         import cellestial as cl
         import scanpy as sc
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         p1 = (
             cl.bar(data, mapping=aes('leiden', fill='predicted_doublet'))
@@ -84,7 +84,7 @@ def bar(
         import cellestial as cl
         import scanpy as sc
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         p2 = (
             cl.bar(data, mapping=aes('cell_type_lvl1', fill='leiden'))

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/single/basic/scatter.py

@@ -73,7 +73,7 @@ def scatter(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         cl.scatter(
             data,
@@ -91,7 +91,7 @@ def scatter(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
 
         cl.scatter(
@@ -109,7 +109,7 @@ def scatter(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
 
         cl.scatter(

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/single/common/xyplot.py

@@ -107,7 +107,7 @@ def xyplot(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         cl.xyplot(
             data,
@@ -126,7 +126,7 @@ def xyplot(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         cl.xyplot(
             data,
@@ -145,7 +145,7 @@ def xyplot(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         cl.xyplot(
             data,

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/single/common/xyplots.py

@@ -148,7 +148,7 @@ def xyplots(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         cl.xyplots(
             data,
@@ -169,7 +169,7 @@ def xyplots(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         cl.xyplots(
             data,

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/single/core/dimensional.py

@@ -59,7 +59,7 @@ def dimensional(
     color_low: str = "#e6e6e6",
     color_mid: str | None = None,
     color_high: str = "#377eb8",
-    mid_point: Literal["mean", "median", "mid"] | float = "median",
+    midpoint: Literal["mean", "median", "mid"] | float = "median",
     axis_type: Literal["axis", "arrow"] | None = None,
     arrow_length: float = 0.25,
     arrow_size: float = 1,
@@ -129,7 +129,7 @@ def dimensional(
         The color to use for the middle part of the color gradient.
     color_high : str, default='#377EB8'
         The color to use for the high end of the color gradient.
-    mid_point : {'mean', 'median', 'mid'} | float, default='median'
+    midpoint : {'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).
         - If 'mean', the midpoint is the mean of the data.
@@ -200,7 +200,7 @@ def dimensional(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         cl.dimensional(data,key="cell_type_lvl1",axis_type="arrow",legend_ondata=True)
 
@@ -213,7 +213,7 @@ def dimensional(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         cl.dimensional(data,key="CD14",axis_type="arrow",color_high="red")
 
@@ -332,7 +332,7 @@ def dimensional(
                 color_low=color_low,
                 color_mid=color_mid,
                 color_high=color_high,
-                mid_point=mid_point,
+                midpoint=midpoint,
             )
         # else: let letsplot handle it
 

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/single/core/distribution.py

@@ -144,7 +144,7 @@ def violin(
 
         from lets_plot import *
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         violin = (
             cl.violin(
@@ -173,7 +173,7 @@ def violin(
 
         from lets_plot import *
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         violin = (
             cl.violin(
@@ -203,7 +203,7 @@ def violin(
 
         from lets_plot import *
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         violin = (
             cl.violin(
@@ -383,7 +383,7 @@ def boxplot(
 
         from lets_plot import *
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         boxplot = (
             cl.boxplot(
@@ -410,7 +410,7 @@ def boxplot(
 
         from lets_plot import *
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         boxplot = (
             cl.boxplot(
@@ -438,7 +438,7 @@ def boxplot(
 
         from lets_plot import *
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         boxplot = (
             cl.boxplot(
@@ -596,7 +596,7 @@ def histogram(
 
         from lets_plot import *
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         histogram = (
             cl.histogram(data, "n_genes_by_counts", bins=50)

{cellestial-0.58.2 → cellestial-0.59.0}/cellestial/single/core/distributions.py

@@ -33,6 +33,7 @@ def violins(
     axis: Literal[0, 1] | None = None,
     color: str | None = None,
     fill: str | None = None,
+    threshold: float | None = None,
     add_keys: Sequence[str] | str | None = None,
     tooltips: Literal["none"] | Sequence[str] | FeatureSpec | None = None,
     geom_fill: str | None = None,
@@ -41,6 +42,7 @@ def violins(
     point_alpha: float = 0.7,
     point_size: float = 0.5,
     point_geom: Literal["jitter", "point", "sina"] = "jitter",
+    point_mapping: FeatureSpec | None = None,
     observations_name: str = "Barcode",
     variables_name: str = "Variable",
     show_points: bool = True,
@@ -97,6 +99,8 @@ def violins(
         Fill aesthetic to split the violin plot (categorical).
         Shortcut for mapping=aes(fill=...)
         e,g., 'cell_type' or 'leiden'.
+    threshold : float | None, default=None
+        If provided, filters out rows where the value column is below the threshold.
     add_keys : Sequence[str] | str | None, default=None
         Additional keys to include in the dataframe.
     tooltips: {'none'} | Sequence[str] | FeatureSpec | None, default=None
@@ -115,11 +119,11 @@ def violins(
         Size for the points in the violin plot.
     point_geom : {'jitter','point','sina'}, default is 'jitter'
         Geom type of the points, default is geom_jitter.
-    trim : bool, default=False
-        Whether to trim the violin plot.
+    point_mapping : FeatureSpec | None, default=None
+        Additional aesthetic mappings for the points, the result of `aes()`.
     observations_name : str, default='Barcode'
         The name to give to barcode (or index) column in the dataframe.
-    variables_name : str, default='Gene'
+    variables_name : str, default='Variable'
         The name to give to variable index column in the dataframe.
     show_points : bool, default=True
         Whether to show points.
@@ -154,10 +158,10 @@ def violins(
         Cell horizontal spacing in px.
     vspace : float | None, default=None
         Cell vertical spacing in px.
-    fit : bool, default=True
+    fit : bool | None, default=None
         Whether to stretch each plot to match the aspect ratio of its cell (fit=True),
         or to preserve the original aspect ratio of plots (fit=False).
-    align : bool, default=False
+    align : bool | None, default=None
         If True, align inner areas (i.e. “geom” bounds) of plots.
         However, cells containing other (sub)grids are not participating
         in the plot “inner areas” layouting.
@@ -200,7 +204,7 @@ def violins(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         cl.violins(
             data,
@@ -226,6 +230,14 @@ def violins(
         variable_keys=variable_keys,
         axis=axis,
     )
+    _collect_aes_columns(
+        data,
+        keys=[],
+        mapping=point_mapping,
+        metadata_columns=metadata_columns,
+        variable_keys=variable_keys,
+        axis=axis,
+    )
     # Tooltips are shared across subplots; pull their fields into the shared
     # frame so each subplot's unpivot index can keep them.
     _resolve_tooltips(
@@ -260,6 +272,7 @@ def violins(
             axis=axis,
             color=color,
             fill=fill,
+            threshold=threshold,
             add_keys=add_keys,
             tooltips=tooltips,
             geom_fill=geom_fill,
@@ -268,6 +281,7 @@ def violins(
             point_alpha=point_alpha,
             point_size=point_size,
             point_geom=point_geom,
+            point_mapping=point_mapping,
             observations_name=observations_name,
             variables_name=variables_name,
             show_points=show_points,
@@ -319,6 +333,7 @@ def boxplots(
     axis: Literal[0, 1] | None = None,
     color: str | None = None,
     fill: str | None = None,
+    threshold: float | None = None,
     add_keys: Sequence[str] | str | None = None,
     tooltips: Literal["none"] | Sequence[str] | FeatureSpec | None = None,
     geom_fill: str | None = None,
@@ -327,6 +342,7 @@ def boxplots(
     point_alpha: float = 0.7,
     point_size: float = 0.5,
     point_geom: Literal["jitter", "point", "sina"] = "jitter",
+    point_mapping: FeatureSpec | None = None,
     observations_name: str = "Barcode",
     variables_name: str = "Variable",
     show_points: bool = True,
@@ -383,6 +399,8 @@ def boxplots(
         Fill aesthetic to split the boxplot (categorical).
         Shortcut for mapping=aes(fill=...)
         e,g., 'cell_type' or 'leiden'.
+    threshold : float | None, default=None
+        If provided, filters out rows where the value column is below the threshold.
     add_keys : Sequence[str] | str | None, default=None
         Additional keys to include in the dataframe.
     tooltips: {'none'} | Sequence[str] | FeatureSpec | None, default=None
@@ -401,9 +419,11 @@ def boxplots(
         Size for the points in the boxplot.
     point_geom : {'jitter','point','sina'}, default is 'jitter'
         Geom type of the points, default is geom_jitter.
+    point_mapping : FeatureSpec | None, default=None
+        Additional aesthetic mappings for the points, the result of `aes()`.
     observations_name : str, default='Barcode'
         The name to give to barcode (or index) column in the dataframe.
-    variables_name : str, default='Gene'
+    variables_name : str, default='Variable'
         The name to give to variable index column in the dataframe.
     show_points : bool, default=True
         Whether to show points.
@@ -437,10 +457,10 @@ def boxplots(
         Cell horizontal spacing in px.
     vspace : float | None, default=None
         Cell vertical spacing in px.
-    fit : bool, default=True
+    fit : bool | None, default=None
         Whether to stretch each plot to match the aspect ratio of its cell (fit=True),
         or to preserve the original aspect ratio of plots (fit=False).
-    align : bool, default=False
+    align : bool | None, default=None
         If True, align inner areas (i.e. “geom” bounds) of plots.
         However, cells containing other (sub)grids are not participating
         in the plot “inner areas” layouting.
@@ -483,7 +503,7 @@ def boxplots(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         cl.boxplots(
             data,
@@ -509,6 +529,14 @@ def boxplots(
         variable_keys=variable_keys,
         axis=axis,
     )
+    _collect_aes_columns(
+        data,
+        keys=[],
+        mapping=point_mapping,
+        metadata_columns=metadata_columns,
+        variable_keys=variable_keys,
+        axis=axis,
+    )
     # Tooltips are shared across subplots; pull their fields into the shared
     # frame so each subplot's unpivot index can keep them.
     _resolve_tooltips(
@@ -543,6 +571,7 @@ def boxplots(
             axis=axis,
             color=color,
             fill=fill,
+            threshold=threshold,
             add_keys=add_keys,
             tooltips=tooltips,
             geom_fill=geom_fill,
@@ -551,6 +580,7 @@ def boxplots(
             point_alpha=point_alpha,
             point_size=point_size,
             point_geom=point_geom,
+            point_mapping=point_mapping,
             observations_name=observations_name,
             variables_name=variables_name,
             show_points=show_points,
@@ -605,6 +635,7 @@ def histograms(
     fill: str | None = None,
     bins: int | None = None,
     binwidth: float | None = None,
+    threshold: float | None = None,
     add_keys: Sequence[str] | str | None = None,
     tooltips: Literal["none"] | Sequence[str] | FeatureSpec | None = None,
     geom_fill: str | None = None,
@@ -665,6 +696,8 @@ def histograms(
         Number of bins. Overridden by `binwidth` if both are provided.
     binwidth : float | None, default=None
         Width of each bin. Takes precedence over `bins`.
+    threshold : float | None, default=None
+        If provided, filters out rows where the value column is below the threshold.
     add_keys : Sequence[str] | str | None, default=None
         Additional keys to include in the dataframe.
     tooltips: {'none'} | Sequence[str] | FeatureSpec | None, default=None
@@ -709,10 +742,10 @@ def histograms(
         Cell horizontal spacing in px.
     vspace : float | None, default=None
         Cell vertical spacing in px.
-    fit : bool, default=True
+    fit : bool | None, default=None
         Whether to stretch each plot to match the aspect ratio of its cell (fit=True),
         or to preserve the original aspect ratio of plots (fit=False).
-    align : bool, default=False
+    align : bool | None, default=None
         If True, align inner areas (i.e. "geom" bounds) of plots.
         However, cells containing other (sub)grids are not participating
         in the plot "inner areas" layouting.
@@ -748,7 +781,7 @@ def histograms(
 
         import cellestial as cl
 
-        data = cl.datasets.pbmc3k(cache_directory="data")
+        data = cl.datasets.pbmc3k()
 
         cl.histograms(
             data,
@@ -810,6 +843,7 @@ def histograms(
             fill=fill,
             bins=bins,
             binwidth=binwidth,
+            threshold=threshold,
             add_keys=add_keys,
             tooltips=tooltips,
             geom_fill=geom_fill,