marsilea 0.5.5__py3-none-any.whl → 0.5.6__py3-none-any.whl

marsilea/_version.py

@@ -1 +1 @@
-version = "0.5.5"
+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/plotter/mesh.py

@@ -577,7 +577,6 @@ class SizedMesh(MeshBase):
         self.alpha = alpha
         self.frameon = frameon
 
-        self.edgecolor = None
         if edgecolor is not None:
             if is_color_like(edgecolor):
                 self.edgecolor = np.repeat(edgecolor, size.size).reshape(size.shape)
@@ -593,6 +592,9 @@ class SizedMesh(MeshBase):
                 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
@@ -601,6 +603,7 @@ class SizedMesh(MeshBase):
         self.kwargs = kwargs
 
         self._collections = None
+        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)
@@ -624,6 +627,8 @@ class SizedMesh(MeshBase):
         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,
@@ -642,7 +647,7 @@ class SizedMesh(MeshBase):
                 unique_ecs = np.unique(self.edgecolor)
                 if len(self.edgecolor_legend_text) == len(unique_ecs):
                     legend_items = [
-                        ("circle", text, dict(ec=ec, fc="none"))
+                        ("circle", text, dict(ec=ec, fc="none", lw=self.linewidth))
                         for text, ec in zip(self.edgecolor_legend_text, unique_ecs)
                     ]
                     ec_legend = ListLegend(
@@ -654,8 +659,7 @@ class SizedMesh(MeshBase):
                         "If edgecolor legend text is provided, the number of unique edgecolors "
                         "must match the number of texts"
                     )
-
-        if self._has_colormesh & (self.color != "none"):
+        if self._has_colormesh & (self._transparent_marker):
             if self.palette is not None:
                 labels, colors = [], []
                 for label, c in self.palette.items():
@@ -708,9 +712,9 @@ class SizedMesh(MeshBase):
             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-0.5.5.dist-info → marsilea-0.5.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: marsilea
-Version: 0.5.5
+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-0.5.5.dist-info → marsilea-0.5.6.dist-info}/RECORD

@@ -1,8 +1,8 @@
 marsilea/__init__.py,sha256=mMtII0QzSVGrr1vJXTglr6wBd2AHElrDnDp1iGQbOxo,626
 marsilea/_api.py,sha256=tymWZHfjhx8-0NNd9762znfdIu36NrARRweEIr5L1mA,283
 marsilea/_deform.py,sha256=QRz4OGXMsQzbiIkC3ASzZayMPhHhoFsEK38oBzSeQG8,14440
-marsilea/_version.py,sha256=v9c8T1qB0Dxuq0vdkPvh2bpcAlRxlK4BxHPcACDymFw,18
-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
@@ -20,13 +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=t9odi21DtrcSmoBQWtYyqmX5_gYDb4wNZQH_VrBjrtY,27190
+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-0.5.5.dist-info/METADATA,sha256=k47nj_h3fBERMN2AXbhVg9yZkrNujRnDVIASpTk1qKE,7265
-marsilea-0.5.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-marsilea-0.5.5.dist-info/licenses/LICENSE,sha256=RhHHDuP61qzKmfHtOQUVLZfCgMkKx9PXzxzkLtmAjHo,1078
-marsilea-0.5.5.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