marsilea 0.5.0rc1__py3-none-any.whl → 0.5.2__py3-none-any.whl

marsilea/__init__.py

@@ -1,6 +1,6 @@
 """Declarative creation of composable visualization"""
 
-__version__ = "0.5.0rc1"
+__version__ = "0.5.2"
 
 import marsilea.plotter as plotter
 from ._deform import Deformation

marsilea/base.py

@@ -1142,142 +1142,6 @@ class ClusterBoard(WhiteBoard):
                 rasterized=rasterized,
             )
 
-    def hsplit(self, cut=None, labels=None, order=None, spacing=0.01):
-        """Split the main canvas horizontally
-
-        .. deprecated:: 0.5.0
-            Use :meth:`~marsilea.base.ClusterBoard.cut_rows` \
-            or :meth:`~marsilea.base.ClusterBoard.group_rows` instead
-
-        Parameters
-        ----------
-        cut : array-like, optional
-            The index of your data to specify where to split the canvas
-        labels : array-like, optional
-            The labels of your data, must be the same length as the data
-        order : array-like, optional
-            The order of the unique labels
-        spacing : float, optional
-            The spacing between each split chunks, default is 0.01
-
-        Examples
-        --------
-        Split the canvas by the unique labels
-
-        .. plot::
-            :context: close-figs
-
-            >>> data = np.random.rand(10, 11)
-            >>> import marsilea as ma
-            >>> h = ma.Heatmap(data)
-            >>> labels = ["A", "B", "C", "A", "B", "C", "A", "B", "C", "A"]
-            >>> h.hsplit(labels=labels, order=["A", "B", "C"])
-            >>> h.add_left(ma.plotter.Labels(labels), pad=.1)
-            >>> h.render()
-
-
-        Split the canvas by the index
-
-        .. plot::
-            :context: close-figs
-
-            >>> h = ma.Heatmap(data)
-            >>> h.hsplit(cut=[4, 8])
-            >>> h.render()
-
-
-        """
-        warnings.warn(
-            DeprecationWarning(
-                "`hsplit` will be deprecated in v0.5.0, use `cut_rows` or `group_rows` instead"
-            ),
-            stacklevel=2,
-        )
-        if self._split_row:
-            raise SplitTwice(axis="horizontally")
-        self._split_row = True
-
-        deform = self.get_deform()
-        deform.hspace = spacing
-        if cut is not None:
-            deform.set_split_row(breakpoints=cut)
-        else:
-            labels = np.asarray(labels)
-
-            reindex, order = reorder_index(labels, order=order)
-            deform.set_data_row_reindex(reindex)
-
-            breakpoints = get_breakpoints(labels[reindex])
-            deform.set_split_row(breakpoints=breakpoints, order=order)
-
-    def vsplit(self, cut=None, labels=None, order=None, spacing=0.01):
-        """Split the main canvas vertically
-
-        .. deprecated:: 0.5.0
-            Use :meth:`~marsilea.base.ClusterBoard.cut_cols` \
-            or :meth:`~marsilea.base.ClusterBoard.group_cols` instead
-
-        Parameters
-        ----------
-        cut : array-like, optional
-            The index of your data to specify where to split the canvas
-        labels : array-like, optional
-            The labels of your data, must be the same length as the data
-        order : array-like, optional
-            The order of the unique labels
-        spacing : float, optional
-            The spacing between each split chunks, default is 0.01
-
-        Examples
-        --------
-        Split the canvas by the unique labels
-
-        .. plot::
-            :context: close-figs
-
-            >>> data = np.random.rand(10, 11)
-            >>> import marsilea as ma
-            >>> h = ma.Heatmap(data)
-            >>> labels = ["A", "B", "C", "A", "B", "C", "A", "B", "C", "A", "B"]
-            >>> h.vsplit(labels=labels, order=["A", "B", "C"])
-            >>> h.add_top(ma.plotter.Labels(labels), pad=.1)
-            >>> h.render()
-
-
-        Split the canvas by the index
-
-        .. plot::
-            :context: close-figs
-
-            >>> h = ma.Heatmap(data)
-            >>> h.vsplit(cut=[4, 8])
-            >>> h.render()
-
-
-        """
-        warnings.warn(
-            DeprecationWarning(
-                "`vsplit` will be deprecated in v0.5.0, use `cut_cols` or `group_cols` instead"
-            ),
-            stacklevel=2,
-        )
-        if self._split_col:
-            raise SplitTwice(axis="vertically")
-        self._split_col = True
-
-        deform = self.get_deform()
-        deform.wspace = spacing
-        if cut is not None:
-            deform.set_split_col(breakpoints=cut)
-        else:
-            labels = np.asarray(labels)
-
-            reindex, order = reorder_index(labels, order=order)
-            deform.set_data_col_reindex(reindex)
-
-            breakpoints = get_breakpoints(labels[reindex])
-            deform.set_split_col(breakpoints=breakpoints, order=order)
-
     def group_rows(self, group, order=None, spacing=0.01):
         """Group rows into chunks
 

marsilea/plotter/_utils.py

@@ -10,12 +10,12 @@ def _format_labels(labels, fmt):
 
 
 def _format_label(a, fmt):
-    if np.isnan(a):
-        a = ""
     if isinstance(fmt, str):
         label = _auto_format_str(fmt, a)
     elif callable(fmt):
         label = fmt(a)
+    elif np.isnan(a):
+        a = ""
     else:
         raise TypeError("fmt must be a str or callable")
     return label

marsilea/upset.py

@@ -239,8 +239,8 @@ class UpsetData:
             marks = marks & (sets_table["cardinality"] <= max_cardinality)
         if min_degree is not None:
             marks = marks & (sets_table["degree"] >= min_degree)
-        if min_degree is not None:
-            marks = marks & (sets_table["degree"] >= max_degree)
+        if max_degree is not None:
+            marks = marks & (sets_table["degree"] <= max_degree)
         return marks
 
     def reset(self):
@@ -561,6 +561,7 @@ class Upset(WhiteBoard):
         self._legend_entries = []
         self._add_intersections = add_intersections
         self._intersection_bar = None
+        self._intersection_bar_side = None
         self._sets_size_bar = None
 
         if orient not in ["h", "v"]:
@@ -732,6 +733,7 @@ class Upset(WhiteBoard):
         )
         data = self.data.cardinality()
         self._intersection_bar = Numbers(data, color=self.color)
+        self._intersection_bar_side = side
         self.add_plot(side, self._intersection_bar, size=size, pad=pad)
 
     def add_sets_size(self, side, pad=0.1, size=1.0, **props):
@@ -956,7 +958,10 @@ class Upset(WhiteBoard):
         self._render_matrix(main_ax)
         # apply highlight style to bar
         if self._add_intersections:
-            for ix, rect in enumerate(self._intersection_bar.bars):
+            bars = self._intersection_bar.bars
+            if self._intersection_bar_side in {"left", "right"}:
+                bars = bars[::-1]
+            for ix, rect in enumerate(bars):
                 bar_style = self._subset_styles.get(ix)
                 if bar_style is not None:
                     rect.set(**bar_style)

{marsilea-0.5.0rc1.dist-info → marsilea-0.5.2.dist-info}/METADATA

@@ -1,14 +1,13 @@
 Metadata-Version: 2.4
 Name: marsilea
-Version: 0.5.0rc1
+Version: 0.5.2
 Summary: Declarative creation of composable visualizations
 Project-URL: Home, https://github.com/Marsilea-viz/marsilea
 Project-URL: Documentation, https://marsilea.readthedocs.io
-Author: Zhihang Zheng
-Author-email: Yimin Zheng <yzheng@cemm.at>
+Author-email: Yimin Zheng <yzheng@cemm.at>, Zhihang Zheng <zhihang.zheng@connect.polyu.hk>
 License: The MIT License (MIT)
         
-        Copyright (c) 2024 Mr-Milk
+        Copyright (c) 2025 Yimin Zheng
         
         Permission is hereby granted, free of charge, to any person obtaining a copy
         of this software and associated documentation files (the "Software"), to deal
@@ -57,6 +56,8 @@ Description-Content-Type: text/markdown
 ![PyPI - License](https://img.shields.io/pypi/l/marsilea?color=FFD43B&style=flat-square)
 [![DOI](https://img.shields.io/badge/DOI-10.1186%2Fs13059--024--03469--3-blue?color=0098FF&style=flat-square)](https://doi.org/10.1186/s13059-024-03469-3)
 
+[![Gitter](https://img.shields.io/gitter/room/Marsilea/Questions?style=flat-square)](https://app.gitter.im/#/room/#Marsilea:gitter.im)
+
 # Marsilea: Declarative creation of composable visualization!
 
 ---
@@ -104,6 +105,12 @@ If you use Marsilea in your research, please cite the following:
 > 
 > _Genome Biology_ 2025 Jan 06. DOI: [10.1186/s13059-017-1382-0](https://doi.org/10.1186/s13059-024-03469-3)
 
+## Get helps
+
+1. Open an issue
+2. Join us on [Gitter](https://app.gitter.im/#/room/#Marsilea:gitter.im)
+
+
 ## Examples
 
 <table>

{marsilea-0.5.0rc1.dist-info → marsilea-0.5.2.dist-info}/RECORD

@@ -1,18 +1,18 @@
-marsilea/__init__.py,sha256=_eGLcXHTDSPWqHXJEpLBbU9NJ9V2Obemv-GsjsrZOmU,598
+marsilea/__init__.py,sha256=0fpp21uDy2gLto0wOvlbShNTZS-1M9twBFuFumSwwlw,595
 marsilea/_api.py,sha256=tymWZHfjhx8-0NNd9762znfdIu36NrARRweEIr5L1mA,283
 marsilea/_deform.py,sha256=QRz4OGXMsQzbiIkC3ASzZayMPhHhoFsEK38oBzSeQG8,14440
-marsilea/base.py,sha256=WTQ1L2Geyt4KjrWWQMSrS-0Z2do2R7FOdBx5_2W8Z7w,51206
+marsilea/base.py,sha256=CmzuwFu0JzgkNpPdI1SqAnkUxINShjT73hrJpksKjhE,46872
 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=puXLlGGpEqAzaTqadpgpsYmIDPH33WyyHIuysRSqFZQ,12163
 marsilea/layout.py,sha256=yNuGvIDfWjbCksQZO-4aUWSA78LJwBBKF5Z5cthC6fM,39741
-marsilea/upset.py,sha256=JnqV9HYYpoeLt-6yMy0HN_PUSgV-ENasf6vq6HsX3cI,30393
+marsilea/upset.py,sha256=9m4Los-yVvVZOEHg6X-yfOdLA9eUBQdK1A_BkOaLIMA,30602
 marsilea/utils.py,sha256=y_KYs4ToiuKEsiBdmcIVtmxMXFpD4wKiJ0k7iBa11z8,2854
 marsilea/plotter/__init__.py,sha256=la30o20zYiHWN2RzElhS8MMCbGKbDDEe0WHXakq9OBQ,806
 marsilea/plotter/_seaborn.py,sha256=Ahy5id35KV-PZ50rI5lmEpA4Oov51u8w6VVQzVZH6hM,8330
-marsilea/plotter/_utils.py,sha256=Efhdk-TrrAanhbXRiEVWThMYvZ4vVHZMVYMs5X3JvIM,710
+marsilea/plotter/_utils.py,sha256=vRnG7kKddwVgDzAqLB8r5EQrLBG9znOw74wh4GdJBX4,712
 marsilea/plotter/arc.py,sha256=44BKVGvDc_OpghfgEvaiVCovZe7_OwZiM20iepaRMFw,8139
 marsilea/plotter/area.py,sha256=zjjAhvgKHYe9rqzcseqZqhwfpgvzm0w2FRJ_vr9Fxm4,2650
 marsilea/plotter/bar.py,sha256=RWDsNbyCUKbybpsBOgbl43lVZc_ynZmTOevE-CtJ5KE,12354
@@ -25,7 +25,7 @@ marsilea/plotter/text.py,sha256=6S4mnAxLJLMkduKiyor03lPd86oTOJ5TojVREA9oU6s,3746
 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-0.5.0rc1.dist-info/METADATA,sha256=iQf49kl4rB5G0nDjejE6-BGqZ3y8z0pLs7tLrWEeGUs,6996
-marsilea-0.5.0rc1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-marsilea-0.5.0rc1.dist-info/licenses/LICENSE,sha256=2TLD8FnLJqXzg8YBRs7W3VZBwfWfp4ArDfBl-rn96Qc,1074
-marsilea-0.5.0rc1.dist-info/RECORD,,
+marsilea-0.5.2.dist-info/METADATA,sha256=ItfPnIgJLjJRHgNax36iPM48Wwb7DHUvg-P-UZkyMS8,7265
+marsilea-0.5.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+marsilea-0.5.2.dist-info/licenses/LICENSE,sha256=RhHHDuP61qzKmfHtOQUVLZfCgMkKx9PXzxzkLtmAjHo,1078
+marsilea-0.5.2.dist-info/RECORD,,

{marsilea-0.5.0rc1.dist-info → marsilea-0.5.2.dist-info}/licenses/LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2024 Mr-Milk
+Copyright (c) 2025 Yimin Zheng
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal