marsilea 0.5.4__py3-none-any.whl → 0.5.6__py3-none-any.whl

marsilea/__init__.py

@@ -1,6 +1,8 @@
 """Declarative creation of composable visualization"""
 
-__version__ = "0.5.4"
+from ._version import version
+
+__version__ = version
 
 import marsilea.plotter as plotter
 from ._deform import Deformation

marsilea/_version.py

@@ -0,0 +1 @@
+version = "0.5.6"

marsilea/base.py

@@ -440,18 +440,16 @@ class WhiteBoard(LegendMaker):
         self.add_plot("bottom", plot, name, size, pad, legend)
 
     def _render_plan(self):
-        for plan in self._col_plan:
-            axes = self.layout.get_ax(plan.name)
-            plan.render(axes)
+        try:
+            for plan in self._col_plan + self._row_plan:
+                axes = self.layout.get_ax(plan.name)
+                plan.render(axes)
 
-        # render other plots
-        for plan in self._row_plan:
-            axes = self.layout.get_ax(plan.name)
-            plan.render(axes)
-
-        main_ax = self.get_main_ax()
-        for plan in self._get_layers_zorder():
-            plan.render(main_ax)
+            main_ax = self.get_main_ax()
+            for plan in self._get_layers_zorder():
+                plan.render(main_ax)
+        except Exception as e:
+            raise Exception(f"An error occur during rendering of {plan}") from e
 
     def add_layer(self, plot: RenderPlan, zorder=None, name=None, legend=True):
         """Add a plotter to the main canvas
@@ -655,7 +653,8 @@ class WhiteBoard(LegendMaker):
     def save(self, fname, **kwargs):
         """Save the figure to a file
 
-        This will force a re-render of the figure
+        Save the current opened figure to a file, if no figure is open,
+        a render will be performed first.
 
         Parameters
         ----------
@@ -665,7 +664,8 @@ class WhiteBoard(LegendMaker):
             Additional options for saving the figure, will be passed to :meth:`~matplotlib.pyplot.savefig`
 
         """
-        self.render()
+        if self.figure is None:
+            self.render()
         save_options = dict(bbox_inches="tight")
         save_options.update(kwargs)
         self.figure.savefig(fname, **save_options)
@@ -1364,23 +1364,19 @@ class ClusterBoard(WhiteBoard):
 
     def _render_plan(self):
         deform = self.get_deform()
-        for plan in self._col_plan:
-            if plan.allow_split:
-                plan.set_deform(deform)
-            axes = self.layout.get_ax(plan.name)
-            plan.render(axes)
+        try:
+            for plan in self._col_plan + self._row_plan:
+                if plan.allow_split:
+                    plan.set_deform(deform)
+                axes = self.layout.get_ax(plan.name)
+                plan.render(axes)
 
-        # render other plots
-        for plan in self._row_plan:
-            if plan.allow_split:
+            main_ax = self.get_main_ax()
+            for plan in self._get_layers_zorder():
                 plan.set_deform(deform)
-            axes = self.layout.get_ax(plan.name)
-            plan.render(axes)
-
-        main_ax = self.get_main_ax()
-        for plan in self._get_layers_zorder():
-            plan.set_deform(deform)
-            plan.render(main_ax)
+                plan.render(main_ax)
+        except Exception as e:
+            raise Exception(f"An error occur during rending of {plan}") from e
 
     def get_deform(self):
         """Return the deformation object of the cluster data"""

marsilea/layout.py

@@ -461,8 +461,8 @@ class CrossLayout(_MarginMixin):
             y = self.get_side_size("bottom")
             if self.is_composite:
                 return x, y
-            x += self.margin.bottom
-            y += self.margin.left
+            x += self.margin.left
+            y += self.margin.bottom
             return x, y
         else:
             return self.anchor

marsilea/plotter/mesh.py

@@ -1,14 +1,21 @@
 __all__ = ["ColorMesh", "Colors", "SizedMesh", "MarkerMesh", "TextMesh", "PatchMesh"]
 
-import numpy as np
-import pandas as pd
 import warnings
 from itertools import cycle
-from legendkit import ColorArt, CatLegend, SizeLegend
-from matplotlib.cm import ScalarMappable
-from matplotlib.colors import ListedColormap, TwoSlopeNorm, Normalize, is_color_like
 from typing import Mapping
 
+import numpy as np
+import pandas as pd
+from legendkit import ColorArt, CatLegend, SizeLegend, ListLegend
+from matplotlib.cm import ScalarMappable
+from matplotlib.colors import (
+    ListedColormap,
+    TwoSlopeNorm,
+    Normalize,
+    is_color_like,
+    to_hex,
+)
+
 from ._utils import _format_label
 from .base import RenderPlan
 from ..layout import close_ticks
@@ -426,8 +433,9 @@ class SizedMesh(MeshBase):
         The range of the size of elements
     size_norm : :class:`matplotlib.colors.Normalize`
         A Normalize instance to map size
-    edgecolor : color
-        The border color of each elements
+    edgecolor : color or array of colors
+        The border color of each elements, if you want to control every element,
+        please supply a 2d array with the same shape as input.
     linewidth : float
         The width of the border of each elements
     frameon : bool
@@ -454,6 +462,10 @@ class SizedMesh(MeshBase):
         Control the size legend, See :class:`legendkit.size_legend`
     color_legend_kws : dict
         Control the color legend, See :class:`legendkit.colorart`
+    edgecolor_legend_text : list of str
+        The texts for the edgecolor legend
+    edgecolor_legend_kws : dict
+        Control the edgecolor legend, See :class:`legendkit.legend`
     kwargs : dict
         Pass to :meth:`matplotlib.axes.Axes.scatter`
 
@@ -511,6 +523,8 @@ class SizedMesh(MeshBase):
         legend=True,
         size_legend_kws=None,
         color_legend_kws=None,
+        edgecolor_legend_text=None,
+        edgecolor_legend_kws=None,
         **kwargs,
     ):
         # normalize size
@@ -528,6 +542,11 @@ class SizedMesh(MeshBase):
         self.legend = legend
         self.color_legend_kws = {} if color_legend_kws is None else color_legend_kws
         self.size_legend_kws = {} if size_legend_kws is None else size_legend_kws
+        self.edgecolor_legend_text = edgecolor_legend_text
+        self.edgecolor_legend_kws = (
+            {} if edgecolor_legend_kws is None else edgecolor_legend_kws
+        )
+
         self._has_colormesh = False
         # process color
         # By default, the circles colors are uniform
@@ -557,7 +576,25 @@ class SizedMesh(MeshBase):
                 self._has_colormesh = True
         self.alpha = alpha
         self.frameon = frameon
-        self.edgecolor = edgecolor
+
+        if edgecolor is not None:
+            if is_color_like(edgecolor):
+                self.edgecolor = np.repeat(edgecolor, size.size).reshape(size.shape)
+                self._single_edgecolor = True
+            else:
+                edgecolor = np.asarray(edgecolor)
+                if edgecolor.shape != self.size_matrix.shape:
+                    raise ValueError(
+                        "If use multiple edgecolors, "
+                        "the shape must be the same as input size"
+                    )
+                # Covert to hex
+                edgecolor = [[to_hex(c) for c in row] for row in edgecolor]
+                self.edgecolor = np.asarray(edgecolor)
+                self._single_edgecolor = False
+        else:
+            self.edgecolor = np.full_like(size, "#00000000", dtype=object)
+            self._single_edgecolor = True
         self.linewidth = linewidth
         self.set_label(label, label_loc, label_props)
         self.grid = grid
@@ -566,7 +603,12 @@ class SizedMesh(MeshBase):
         self.kwargs = kwargs
 
         self._collections = None
-        self.set_data(self.size_matrix, self.color2d)
+        self._transparent_marker = "none" in self.color2d
+        render_data = [self.size_matrix, self.color2d]
+        if self.edgecolor is not None:
+            render_data.append(self.edgecolor)
+
+        self.set_data(*render_data)
 
     def update_main_canvas_size(self):
         return get_canvas_size_by_data(self.orig_size.shape)
@@ -574,11 +616,20 @@ class SizedMesh(MeshBase):
     def get_legends(self):
         if not self.legend:
             return None
+
+        legends = []
+
         if self.color is not None:
             size_color = self.color
         else:
             size_color = "black"
-        handler_kw = dict(edgecolor=self.edgecolor, linewidth=self.linewidth)
+        edgecolor = None
+        if self.edgecolor is not None:
+            if self._single_edgecolor:
+                edgecolor = self.edgecolor.flatten()[0]
+        if self._transparent_marker & (edgecolor is None):
+            edgecolor = "black"
+        handler_kw = dict(edgecolor=edgecolor, linewidth=self.linewidth)
         options = dict(
             colors=size_color,
             handle=self.marker,
@@ -588,8 +639,27 @@ class SizedMesh(MeshBase):
         )
         options.update(self.size_legend_kws)
         size_legend = SizeLegend(self.size_matrix, array=self.orig_size, **options)
-
-        if self._has_colormesh & (self.color != "none"):
+        legends.append(size_legend)
+
+        # Construct edgecolor legend
+        if self.edgecolor is not None:
+            if self.edgecolor_legend_text is not None:
+                unique_ecs = np.unique(self.edgecolor)
+                if len(self.edgecolor_legend_text) == len(unique_ecs):
+                    legend_items = [
+                        ("circle", text, dict(ec=ec, fc="none", lw=self.linewidth))
+                        for text, ec in zip(self.edgecolor_legend_text, unique_ecs)
+                    ]
+                    ec_legend = ListLegend(
+                        legend_items=legend_items, **self.color_legend_kws
+                    )
+                    legends.append(ec_legend)
+                else:
+                    raise ValueError(
+                        "If edgecolor legend text is provided, the number of unique edgecolors "
+                        "must match the number of texts"
+                    )
+        if self._has_colormesh & (self._transparent_marker):
             if self.palette is not None:
                 labels, colors = [], []
                 for label, c in self.palette.items():
@@ -606,16 +676,20 @@ class SizedMesh(MeshBase):
             else:
                 ScalarMappable(norm=self.norm, cmap=self.cmap)
                 color_legend = ColorArt(self._collections, **self.color_legend_kws)
-            return [size_legend, color_legend]
+            legends.append(color_legend)
+
+        if len(legends) == 1:
+            return legends[0]
         else:
-            return size_legend
+            return legends
 
     def render_ax(self, spec):
         ax = spec.ax
-        size, color = spec.data
+        size, color, edgecolors = spec.data
         if self.is_flank:
             size = size.T
             color = color.T
+            edgecolors = edgecolors.T
         Y, X = size.shape
         xticks = np.arange(X) + 0.5
         yticks = np.arange(Y) + 0.5
@@ -633,14 +707,14 @@ class SizedMesh(MeshBase):
 
         options = dict(
             s=size,
-            edgecolor=self.edgecolor,
+            edgecolors=edgecolors.flatten(),
             linewidths=self.linewidth,
             marker=self.marker,
         )
         if self.color is not None:
-            options["c"] = color
+            options["c"] = color.flatten()
         else:
-            options.update(dict(c=color, norm=self.norm, cmap=self.cmap))
+            options.update(dict(c=color.flatten(), norm=self.norm, cmap=self.cmap))
         self._collections = ax.scatter(xv, yv, **options, **self.kwargs)
 
         close_ticks(ax)

{marsilea-0.5.4.dist-info → marsilea-0.5.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: marsilea
-Version: 0.5.4
+Version: 0.5.6
 Summary: Declarative creation of composable visualizations
 Project-URL: Home, https://github.com/Marsilea-viz/marsilea
 Project-URL: Documentation, https://marsilea.readthedocs.io

{marsilea-0.5.4.dist-info → marsilea-0.5.6.dist-info}/RECORD

@@ -1,13 +1,14 @@
-marsilea/__init__.py,sha256=Ml3xgdyN-IinhsaejVadUjIURHJzg8fhi2Y_uERAuI8,595
+marsilea/__init__.py,sha256=mMtII0QzSVGrr1vJXTglr6wBd2AHElrDnDp1iGQbOxo,626
 marsilea/_api.py,sha256=tymWZHfjhx8-0NNd9762znfdIu36NrARRweEIr5L1mA,283
 marsilea/_deform.py,sha256=QRz4OGXMsQzbiIkC3ASzZayMPhHhoFsEK38oBzSeQG8,14440
-marsilea/base.py,sha256=CmzuwFu0JzgkNpPdI1SqAnkUxINShjT73hrJpksKjhE,46872
+marsilea/_version.py,sha256=FtfC8ptaFH0Unc72bPRynMH_N62bxa4tnazGgIcgnTY,18
+marsilea/base.py,sha256=GBgSirueH65nhfkunCVYhV7ePX4i01jog5gzkBBOsi0,46951
 marsilea/dataset.py,sha256=Qh8k1DhTiwP_Me709CkpNwRaYLDzlenRTIk0U6D58_g,4631
 marsilea/dendrogram.py,sha256=Ung43zseybZKzTEvH5P_ge3WGfsr7i7qsX7YEVDlC74,15590
 marsilea/exceptions.py,sha256=wN5ElUZxuaJKSnnwWdkNx6P-Oc16dzSuaRPbRKWIBEM,1046
 marsilea/heatmap.py,sha256=8Wo1NxFTBp1a7NOISmer0yQYWWgf51Xsvjav1h1vTYk,4316
 marsilea/layers.py,sha256=w_yvghwYAO112mVvp1krjUjEIQYq_1nz2uCsTUJdB-Y,12909
-marsilea/layout.py,sha256=yNuGvIDfWjbCksQZO-4aUWSA78LJwBBKF5Z5cthC6fM,39741
+marsilea/layout.py,sha256=b6aynXl2senRYjaYnNikjIzK84RkXaBvAyt86VRWw-g,39741
 marsilea/upset.py,sha256=9m4Los-yVvVZOEHg6X-yfOdLA9eUBQdK1A_BkOaLIMA,30602
 marsilea/utils.py,sha256=y_KYs4ToiuKEsiBdmcIVtmxMXFpD4wKiJ0k7iBa11z8,2854
 marsilea/plotter/__init__.py,sha256=la30o20zYiHWN2RzElhS8MMCbGKbDDEe0WHXakq9OBQ,806
@@ -19,13 +20,13 @@ marsilea/plotter/bar.py,sha256=RWDsNbyCUKbybpsBOgbl43lVZc_ynZmTOevE-CtJ5KE,12354
 marsilea/plotter/base.py,sha256=b_NmrW_oNPc-HwQsjx1NsC2lknYK6qSaDp_7SxeoUEM,18938
 marsilea/plotter/bio.py,sha256=34tucmxs4LM3TFZoGsrjnXTolyrzYaHVEiRe4dzDH68,5040
 marsilea/plotter/images.py,sha256=gb0xIQhUch3rNAt3FfvuUoamSGEynoBBBky2eE754ec,9560
-marsilea/plotter/mesh.py,sha256=D6snenMjQ-rM9g3O4PGelSiaBNKmY2OPZU5onILlmO0,24530
+marsilea/plotter/mesh.py,sha256=ARDPWrQLbdIS22B7Ct_aYPXY7IxwVKcICdBBhg8UplE,27482
 marsilea/plotter/range.py,sha256=sXWKrvpq7nU7giiHPjayM7h9Q7gblhjXxHm8ioB3cm4,3770
 marsilea/plotter/text.py,sha256=6S4mnAxLJLMkduKiyor03lPd86oTOJ5TojVREA9oU6s,37466
 oncoprinter/__init__.py,sha256=efshcAD1h9s-NVJj4HLU9-hXc_LtTeIrNYqLHl-sm_g,106
-oncoprinter/core.py,sha256=5KPnKW5ivlxPp14uJd0OtfTv-pXV2UEym8EbII2VCcw,11846
-oncoprinter/preset.py,sha256=mBk2tFCqoTj_1ZZKRYuv4j2I3NTBa6Swc9wjzbmxRVw,8238
-marsilea-0.5.4.dist-info/METADATA,sha256=9SS9_JT6N9FRdBenz-95mnzFY5LVal4lhMocoyvcUsA,7265
-marsilea-0.5.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-marsilea-0.5.4.dist-info/licenses/LICENSE,sha256=RhHHDuP61qzKmfHtOQUVLZfCgMkKx9PXzxzkLtmAjHo,1078
-marsilea-0.5.4.dist-info/RECORD,,
+oncoprinter/core.py,sha256=XBIwTsAvcA-mJSwHU0xpaTBCxBNh7yusmzblRATmekY,11866
+oncoprinter/preset.py,sha256=lo6Llz31KVFt3QOFgFc0BunloZV1FxcFVpH8kOfarNw,8363
+marsilea-0.5.6.dist-info/METADATA,sha256=Ve7qLr7YzOz8bKG10ZIgJHYxPSiGyOXfdhhQrk4oDTE,7265
+marsilea-0.5.6.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+marsilea-0.5.6.dist-info/licenses/LICENSE,sha256=RhHHDuP61qzKmfHtOQUVLZfCgMkKx9PXzxzkLtmAjHo,1078
+marsilea-0.5.6.dist-info/RECORD,,

oncoprinter/core.py

@@ -168,7 +168,7 @@ class GenomicData:
         cs = {}
         for track, df in gb:
             cs[track] = Counter(df["event"])
-        return pd.DataFrame(cs).fillna(0.0)
+        return pd.DataFrame(cs).fillna(0.0).loc[:, self.tracks]
 
     def get_sample_mutation_types(self):
         gb = self.data.groupby("sample", sort=False, observed=True)

oncoprinter/preset.py

@@ -125,6 +125,9 @@ class MatchRule:
 
 MATCH_POOL = {
     Alteration.AMP: MatchRule(startswith="amp"),
+    Alteration.BACKGROUND: MatchRule(
+        contains=["background", "no", "none", "na", "nan", "bg"], flexible=True
+    ),
     Alteration.GAIN: MatchRule(startswith="gain"),
     Alteration.HOMDEL: MatchRule(
         startswith="homdel", contains=["deep", "deletion"], flexible=True