marsilea 0.3.5__tar.gz → 0.4.0__tar.gz

{marsilea-0.3.5 → marsilea-0.4.0}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: marsilea
-Version: 0.3.5
-Summary: Create x-layout visualization
+Version: 0.4.0
+Summary: Declarative creation of composable visualization
 Author: Zhihang Zheng
 Author-email: Mr-Milk <yzheng@cemm.at>
 Requires-Python: >=3.8

{marsilea-0.3.5 → marsilea-0.4.0}/pyproject.toml

@@ -44,5 +44,16 @@ dev = [
     "mpl_fontkit"
 ]
 
+[tool.flit.sdist]
+exclude = [
+    "docs",
+    "app",
+    "data",
+    "img",
+    "tests",
+    "scripts",
+    "readthedocs.yaml",
+]
+
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]

{marsilea-0.3.5 → marsilea-0.4.0}/src/marsilea/__init__.py

@@ -1,12 +1,17 @@
-"""Create x-layout visualization"""
+"""Declarative creation of composable visualization"""
 
-__version__ = "0.3.5"
+__version__ = "0.4.0"
 
 import marsilea.plotter as plotter
 from ._deform import Deformation
-from .base import (WhiteBoard, ClusterBoard,
-                   ZeroWidth, ZeroHeight,
-                   ZeroWidthCluster, ZeroHeightCluster)
+from .base import (
+    WhiteBoard,
+    ClusterBoard,
+    ZeroWidth,
+    ZeroHeight,
+    ZeroWidthCluster,
+    ZeroHeightCluster,
+)
 from .dataset import load_data
 from .dendrogram import Dendrogram, GroupDendrogram
 from .heatmap import Heatmap, SizedHeatmap, CatHeatmap

{marsilea-0.3.5 → marsilea-0.4.0}/src/marsilea/base.py

@@ -46,6 +46,7 @@ def get_breakpoints(arr):
 
 class LegendMaker:
     """The factory class to handle legends"""
+
     layout: CrossLayout | CompositeCrossLayout
     _legend_box: List[Artist] = None
     _legend_name: str = None
@@ -66,34 +67,35 @@ class LegendMaker:
         """
         raise NotImplementedError("Should be implemented in derived class")
 
-    def custom_legend(self, legend, name=None):
+    def custom_legend(self, legend_func, name=None):
         """Add a custom legend
 
         Parameters
         ----------
 
-        legend : `Artist <matplotlib.artist.Artists>`
-            A legend object
+        legend_func : Callable
+            A function that return the legend object,
+            the legend must be an `Artist <matplotlib.artist.Artists>`
         name : str, optional
             The name of the legend
 
         """
         if name is None:
             name = str(uuid4())
-        self._user_legends[name] = [legend]
+        self._user_legends[name] = legend_func
 
     def add_legends(
-            self,
-            side="right",
-            pad=0,
-            order=None,
-            stack_by=None,
-            stack_size=3,
-            align_legends=None,
-            align_stacks=None,
-            legend_spacing=10,
-            stack_spacing=10,
-            box_padding=2,
+        self,
+        side="right",
+        pad=0.0,
+        order=None,
+        stack_by=None,
+        stack_size=3,
+        align_legends=None,
+        align_stacks=None,
+        legend_spacing=10,
+        stack_spacing=10,
+        box_padding=2,
     ):
         """Draw legend based on the order of annotation
 
@@ -128,6 +130,10 @@ class LegendMaker:
             Add pad around the whole legend box
 
         """
+        # TODO: Allow user to control where to add legends,
+        #       relative to the main canvas or the whole figure
+        # TODO: Allow user to add stack_size as a list
+        #       Each stack can contain different number of legends
         _check_side(side)
         self._draw_legend = True
         if stack_by is None:
@@ -154,7 +160,8 @@ class LegendMaker:
         self.layout.remove_legend_ax()
 
     def _legends_drawer(self, ax):
-        legends = {**self.get_legends(), **self._user_legends}
+        user_legends = {k: [v()] for k, v in self._user_legends.items()}
+        legends = {**self.get_legends(), **user_legends}
 
         # force to remove all legends before drawing
         # In case some legends are added implicitly
@@ -236,9 +243,9 @@ class WhiteBoard(LegendMaker):
 
     Parameters
     ----------
-    width : int, optional
+    width : float, optional
         The width of the main canvas in inches
-    height : int, optional
+    height : float, optional
         The height of the main canvas in inches
     name : str, optional
         The name of the main canvas
@@ -305,7 +312,7 @@ class WhiteBoard(LegendMaker):
         super().__init__()
 
     def add_plot(
-            self, side, plot: RenderPlan, name=None, size=None, pad=0.0, legend=True
+        self, side, plot: RenderPlan, name=None, size=None, pad=0.0, legend=True
     ):
         """Add a plotter to the board
 
@@ -676,8 +683,9 @@ class ZeroWidth(WhiteBoard):
     """
 
     def __init__(self, height, name=None, margin=0.2):
-        super().__init__(width=0, height=height, name=name,
-                         margin=margin, init_main=False)
+        super().__init__(
+            width=0, height=height, name=name, margin=margin, init_main=False
+        )
 
 
 class ZeroHeight(WhiteBoard):
@@ -689,8 +697,9 @@ class ZeroHeight(WhiteBoard):
     """
 
     def __init__(self, width, name=None, margin=0.2):
-        super().__init__(width=width, height=0, name=name,
-                         margin=margin, init_main=False)
+        super().__init__(
+            width=width, height=0, name=name, margin=margin, init_main=False
+        )
 
 
 class CompositeBoard(LegendMaker):
@@ -771,9 +780,9 @@ class ClusterBoard(WhiteBoard):
     ----------
     cluster_data : ndarray
         The cluster data
-    width : int, optional
+    width : float, optional
         The width of the main canvas in inches
-    height : int, optional
+    height : float, optional
         The height of the main canvas in inches
     name : str, optional
         The name of the main canvas
@@ -799,13 +808,13 @@ class ClusterBoard(WhiteBoard):
     _mesh = None
 
     def __init__(
-            self,
-            cluster_data,
-            width=None,
-            height=None,
-            name=None,
-            margin=0.2,
-            init_main=True,
+        self,
+        cluster_data,
+        width=None,
+        height=None,
+        name=None,
+        margin=0.2,
+        init_main=True,
     ):
         super().__init__(
             width=width, height=height, name=name, margin=margin, init_main=init_main
@@ -816,24 +825,24 @@ class ClusterBoard(WhiteBoard):
         self._deform = Deformation(cluster_data)
 
     def add_dendrogram(
-            self,
-            side,
-            method=None,
-            metric=None,
-            linkage=None,
-            add_meta=True,
-            add_base=True,
-            add_divider=True,
-            meta_color=None,
-            linewidth=None,
-            colors=None,
-            divider_style="--",
-            meta_ratio=0.2,
-            show=True,
-            name=None,
-            size=0.5,
-            pad=0.0,
-            get_meta_center=None,
+        self,
+        side,
+        method=None,
+        metric=None,
+        linkage=None,
+        add_meta=True,
+        add_base=True,
+        add_divider=True,
+        meta_color=None,
+        linewidth=None,
+        colors=None,
+        divider_style="--",
+        meta_ratio=0.2,
+        show=True,
+        name=None,
+        size=0.5,
+        pad=0.0,
+        get_meta_center=None,
     ):
         """Run cluster and add dendrogram
 
@@ -1031,7 +1040,11 @@ class ClusterBoard(WhiteBoard):
 
 
         """
-        warnings.warn(DeprecationWarning("`hsplit` will be deprecated in v0.5.0, use `cut_rows` or `group_rows` instead"))
+        warnings.warn(
+            DeprecationWarning(
+                "`hsplit` will be deprecated in v0.5.0, use `cut_rows` or `group_rows` instead"
+            )
+        )
         if self._split_row:
             raise SplitTwice(axis="horizontally")
         self._split_row = True
@@ -1094,7 +1107,11 @@ class ClusterBoard(WhiteBoard):
 
 
         """
-        warnings.warn(DeprecationWarning("`vsplit` will be deprecated in v0.5.0, use `cut_cols` or `group_cols` instead"))
+        warnings.warn(
+            DeprecationWarning(
+                "`vsplit` will be deprecated in v0.5.0, use `cut_cols` or `group_cols` instead"
+            )
+        )
         if self._split_col:
             raise SplitTwice(axis="vertically")
         self._split_col = True
@@ -1424,8 +1441,14 @@ class ZeroWidthCluster(ClusterBoard):
     """
 
     def __init__(self, cluster_data, height, name=None, margin=0.2):
-        super().__init__(cluster_data=cluster_data, width=0, height=height,
-                         name=name, margin=margin, init_main=False)
+        super().__init__(
+            cluster_data=cluster_data,
+            width=0,
+            height=height,
+            name=name,
+            margin=margin,
+            init_main=False,
+        )
 
 
 class ZeroHeightCluster(ClusterBoard):
@@ -1448,5 +1471,11 @@ class ZeroHeightCluster(ClusterBoard):
     """
 
     def __init__(self, cluster_data, width, name=None, margin=0.2):
-        super().__init__(cluster_data=cluster_data, width=width, height=0,
-                         name=name, margin=margin, init_main=False)
+        super().__init__(
+            cluster_data=cluster_data,
+            width=width,
+            height=0,
+            name=name,
+            margin=margin,
+            init_main=False,
+        )

{marsilea-0.3.5 → marsilea-0.4.0}/src/marsilea/plotter/__init__.py

@@ -32,5 +32,6 @@ from .base import RenderPlan
 from .bio import SeqLogo
 from .mesh import Colors, ColorMesh, SizedMesh, MarkerMesh, TextMesh
 from .text import Labels, AnnoLabels, Title, Chunk, FixedChunk
+
 # from ._images import Emoji
 from .area import Area

{marsilea-0.3.5 → marsilea-0.4.0}/src/marsilea/plotter/_images.py

@@ -51,13 +51,11 @@ class Emoji(RenderPlan):
         self.mode = mode
 
     def _get_images_bbox(self, figure, imgs):
-
         for img in imgs:
             width, height = img.shape[:2]
 
         return Bbox.from_bounds(0, 0, width, height)
 
-
     def render_ax(self, spec):
         ax = spec.ax
         data = spec.data
@@ -89,9 +87,13 @@ class Emoji(RenderPlan):
                 x0, y0 = ax.transData.transform((loc, loc_y))
                 return Bbox.from_bounds(x0, y0, width, height)
 
-            partial_get_emoji_bbox = partial(get_emoji_bbox, loc=loc, loc_y=loc_y,
-                                             width=fit_scale_width,
-                                             height=fit_scale_height)
+            partial_get_emoji_bbox = partial(
+                get_emoji_bbox,
+                loc=loc,
+                loc_y=loc_y,
+                width=fit_scale_width,
+                height=fit_scale_height,
+            )
 
             i1 = BboxImage(partial_get_emoji_bbox, data=img)
             ax.add_artist(i1)

{marsilea-0.3.5 → marsilea-0.4.0}/src/marsilea/plotter/_seaborn.py

@@ -20,9 +20,11 @@ class _SeabornBase(StatsBase):
         hue_order=None,
         palette=None,
         orient=None,
-        label=None,
         legend_kws=None,
         group_kws=None,
+        label=None,
+        label_loc=None,
+        label_props=None,
         **kwargs,
     ):
         if isinstance(data, Mapping):
@@ -62,7 +64,7 @@ class _SeabornBase(StatsBase):
         self.kws = kwargs
 
         self.orient = orient
-        self.label = label
+        self.set_label(label, label_loc, label_props)
         self.legend_kws = {} if legend_kws is None else legend_kws
         if group_kws is not None:
             self.set_group_params(group_kws)

{marsilea-0.3.5 → marsilea-0.4.0}/src/marsilea/plotter/arc.py

@@ -212,8 +212,8 @@ class Arc(StatsBase):
                         )
 
                         if self.side == "left":
-                            xy = (1, arc_mid)
-                            angle = 90
+                            xy = (0, arc_mid)
+                            angle = -90
                         elif self.side == "right":
                             xy = (0, arc_mid)
                             angle = -90
@@ -233,6 +233,8 @@ class Arc(StatsBase):
             ax.set_xlim(0, 1)
         if self.side == "top":
             ax.invert_yaxis()
+        if self.side == "left":
+            ax.invert_xaxis()
         ax.set_axis_off()
 
     def get_legends(self):

{marsilea-0.3.5 → marsilea-0.4.0}/src/marsilea/plotter/area.py

@@ -42,11 +42,20 @@ class Area(StatsBase):
 
     """
 
-    def __init__(self, data, color=None, add_outline=True, alpha=.4,
-                 linecolor=None, linewidth=1,
-                 group_kws=None, label=None, label_loc=None, label_props=None,
-                 **kwargs):
-
+    def __init__(
+        self,
+        data,
+        color=None,
+        add_outline=True,
+        alpha=0.4,
+        linecolor=None,
+        linewidth=1,
+        group_kws=None,
+        label=None,
+        label_loc=None,
+        label_props=None,
+        **kwargs,
+    ):
         if color is None:
             color = "skyblue"
         if linecolor is None:
@@ -71,22 +80,22 @@ class Area(StatsBase):
         if gp is None:
             gp = {}
 
-        fill_options = {'color': self.color, 'alpha': self.alpha, **self.kws, **gp}
-        line_options = {'color': self.linecolor, 'linewidth': self.linewidth, **gp}
+        fill_options = {"color": self.color, "alpha": self.alpha, **self.kws, **gp}
+        line_options = {"color": self.linecolor, "linewidth": self.linewidth, **gp}
 
         x = np.arange(len(data))
         if self.get_orient() == "h":
             ax.fill_betweenx(x, data, **fill_options)
             if self.add_outline:
                 ax.plot(data, x, **line_options)
-            ax.set_ylim(-.5, len(data)-.5)
+            ax.set_ylim(-0.5, len(data) - 0.5)
             if self.side == "left":
                 ax.invert_xaxis()
         else:
             ax.fill_between(x, data, **fill_options)
             if self.add_outline:
                 ax.plot(x, data, **line_options)
-            ax.set_xlim(-.5, len(data)-.5)
+            ax.set_xlim(-0.5, len(data) - 0.5)
         return ax
 
 

{marsilea-0.3.5 → marsilea-0.4.0}/src/marsilea/plotter/bar.py

@@ -103,6 +103,8 @@ class Numbers(_BarBase):
         show_value=True,
         fmt=None,
         label=None,
+        label_loc=None,
+        label_props=None,
         value_pad=2.0,
         props=None,
         **kwargs,
@@ -114,6 +116,7 @@ class Numbers(_BarBase):
         self._process_params(
             width, orient, show_value, fmt, label, value_pad, props, **kwargs
         )
+        self.set_label(label, label_loc, label_props)
 
     def render_ax(self, spec):
         ax = spec.ax

{marsilea-0.3.5 → marsilea-0.4.0}/src/marsilea/plotter/base.py

@@ -95,6 +95,7 @@ class RenderSpec:
 
 
     """
+
     ax: Axes
 
     data: Any
@@ -271,11 +272,15 @@ class RenderPlan:
         if group_data is not None:
             if self.has_deform:
                 group_data = np.asarray(group_data)
-                if self.deform.is_col_split & self.is_body & self.deform.is_col_cluster:
+                if (
+                    self.deform.is_col_split
+                    & (self.is_body | (self.side == "main"))
+                    & self.deform.is_col_cluster
+                ):
                     return group_data[self.deform.col_chunk_index]
                 elif (
                     self.deform.is_row_split
-                    & self.is_flank
+                    & (self.is_flank | (self.side == "main"))
                     & self.deform.is_row_cluster
                 ):
                     return group_data[self.deform.row_chunk_index]
@@ -610,6 +615,13 @@ class StatsBase(RenderPlan):
             ax.set_xlim(*lims) if is_h else ax.set_ylim(*lims)
 
     def render(self, axes):
+        # check if self._plan_label.loc is None
+        is_loc = False
+        props = None
+        if self._plan_label is not None:
+            if self._plan_label.loc is not None:
+                is_loc = True
+            props = self._plan_label.props
         if self.is_split:
             for spec in self.get_render_spec(axes):
                 self.render_ax(spec)
@@ -619,11 +631,13 @@ class StatsBase(RenderPlan):
                 # leave axis for the first ax
                 if (i == 0) & (self.get_orient() == "v"):
                     self._setup_axis(ax)
-                    ax.set_ylabel(self.label)
+                    if not is_loc:
+                        ax.set_ylabel(self.label, fontdict=props)
                 # leave axis for the last ax
                 elif (i == len(axes) - 1) & (self.get_orient() == "h"):
                     self._setup_axis(ax)
-                    ax.set_xlabel(self.label)
+                    if not is_loc:
+                        ax.set_xlabel(self.label, fontdict=props)
                 else:
                     ax.set_axis_off()
         else:
@@ -632,6 +646,11 @@ class StatsBase(RenderPlan):
             self._setup_axis(axes)
             if self.label is not None:
                 if self.get_orient() == "v":
-                    axes.set_ylabel(self.label)
+                    if not is_loc:
+                        axes.set_ylabel(self.label, fontdict=props)
                 else:
-                    axes.set_xlabel(self.label)
+                    if not is_loc:
+                        axes.set_xlabel(self.label, fontdict=props)
+
+        if self.allow_labeling & is_loc:
+            self._plan_label.add(axes, self.side)

{marsilea-0.3.5 → marsilea-0.4.0}/src/marsilea/plotter/mesh.py

@@ -430,6 +430,12 @@ class SizedMesh(MeshBase):
         The width of the border of each elements
     frameon : bool
         Whether to draw a frame
+    grid : bool
+        Whether to draw grid
+    grid_color : color
+        The color of grid
+    grid_linewidth : float
+        The width of grid line
     palette : dict
         Use to map color if input categorical data
     marker : str
@@ -494,6 +500,9 @@ class SizedMesh(MeshBase):
         edgecolor=None,
         linewidth=1,
         frameon=True,
+        grid=False,
+        grid_color=".8",
+        grid_linewidth=1,
         palette=None,
         marker="o",
         label=None,
@@ -534,8 +543,8 @@ class SizedMesh(MeshBase):
                 if palette is not None:
                     encoder = {}
                     render_colors = []
-                    for i, (label, c) in enumerate(palette.items()):
-                        encoder[label] = i
+                    for i, (plabel, c) in enumerate(palette.items()):
+                        encoder[plabel] = i
                         render_colors.append(c)
                     self.cmap = ListedColormap(render_colors)
                     self.color2d = encode_numeric(color, encoder)
@@ -548,6 +557,9 @@ class SizedMesh(MeshBase):
         self.edgecolor = edgecolor
         self.linewidth = linewidth
         self.set_label(label, label_loc, label_props)
+        self.grid = grid
+        self.grid_color = grid_color
+        self.grid_linewidth = grid_linewidth
         self.kwargs = kwargs
 
         self._collections = None
@@ -606,6 +618,16 @@ class SizedMesh(MeshBase):
         yticks = np.arange(Y) + 0.5
         xv, yv = np.meshgrid(xticks, yticks)
 
+        if self.grid:
+            for x in xticks:
+                ax.axvline(
+                    x, color=self.grid_color, linewidth=self.grid_linewidth, zorder=0
+                )
+            for y in yticks:
+                ax.axhline(
+                    y, color=self.grid_color, linewidth=self.grid_linewidth, zorder=0
+                )
+
         options = dict(
             s=size,
             edgecolor=self.edgecolor,

{marsilea-0.3.5 → marsilea-0.4.0}/src/marsilea/upset.py

@@ -474,7 +474,10 @@ class Upset(WhiteBoard):
         Whether or which side to add the label.
     width : float
     height : float
-    ratio : float
+    size_scale : float
+        The scale of the plot
+    size_aspect : float
+        The aspect ratio of the plot
 
     Examples
     --------
@@ -514,6 +517,8 @@ class Upset(WhiteBoard):
         add_labels=True,
         width=None,
         height=None,
+        size_scale=0.3,
+        size_aspect=1.0,
     ):
         # The modification happens inplace
         upset_data = data
@@ -567,7 +572,11 @@ class Upset(WhiteBoard):
         self.orient = orient
 
         width, height = get_canvas_size_by_data(
-            main_shape, scale=0.3, width=width, height=height, aspect=1
+            main_shape,
+            scale=size_scale,
+            width=width,
+            height=height,
+            aspect=size_aspect,
         )
 
         super().__init__(width=width, height=height)
@@ -717,6 +726,7 @@ class Upset(WhiteBoard):
             raise ValueError(msg)
 
     def add_intersections(self, side, pad=0.1, size=1.0):
+        self._add_intersections = True
         self._check_side(
             side, "Intersections", dict(h=["top", "bottom"], v=["left", "right"])
         )