marsilea 0.4.3__tar.gz → 0.4.5__tar.gz

{marsilea-0.4.3 → marsilea-0.4.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: marsilea
-Version: 0.4.3
+Version: 0.4.5
 Dynamic: Summary
 Project-URL: Home, https://github.com/Marsilea-viz/marsilea
 Author: Zhihang Zheng
@@ -34,7 +34,7 @@ Requires-Python: >=3.8
 Requires-Dist: legendkit
 Requires-Dist: matplotlib>=3.6
 Requires-Dist: numpy
-Requires-Dist: pandas
+Requires-Dist: pandas[parquet]
 Requires-Dist: platformdirs
 Requires-Dist: scipy
 Requires-Dist: seaborn

{marsilea-0.4.3 → marsilea-0.4.5}/pyproject.toml

@@ -20,7 +20,7 @@ requires-python = ">=3.8"
 urls = {Home="https://github.com/Marsilea-viz/marsilea"}
 dependencies = [
     "numpy",
-    "pandas",
+    "pandas[parquet]",
     "matplotlib>=3.6",
     "seaborn",
     "scipy",

{marsilea-0.4.3 → marsilea-0.4.5}/src/marsilea/__init__.py

@@ -1,6 +1,6 @@
 """Declarative creation of composable visualization"""
 
-__version__ = "0.4.3"
+__version__ = "0.4.5"
 
 import marsilea.plotter as plotter
 from ._deform import Deformation

{marsilea-0.4.3 → marsilea-0.4.5}/src/marsilea/dataset.py

@@ -10,15 +10,15 @@ BASE_URL = "https://raw.githubusercontent.com/Marsilea-viz/marsilea-data/main"
 def load_data(name, cache=True):
     """To load marsilea dataset
 
-    - 'cooking_oils': Cooking oils dataset
-    - 'imdb': The IMDB Top 100 Movies
-    - 'pbmc3k': single-cell RNA-seq dataset from 10X Genomics
-    - 'oncoprint': Subsample of Breast Invasive Carcinoma
-                (TCGA, PanCancer Atlas)
-    - 'mouse_embryo': Spatial mapping of mouse embryo at E12.5
-    - 'seq_align': Sequence alignment data
-    - 'les_miserables': Characters in Les Misérables
-    - 'sc_multiomics': Single-cell multi-omics dataset from COVID-19 patients
+    - `cooking_oils`: Cooking oils dataset
+    - `imdb`: The IMDB Top 100 Movies
+    - `pbmc3k`: single-cell RNA-seq dataset from 10X Genomics
+    - `oncoprint`: Subsample of Breast Invasive Carcinoma (TCGA, PanCancer Atlas)
+    - `mouse_embryo`: Spatial mapping of mouse embryo at E12.5
+    - `seq_align`: Sequence alignment data
+    - `les_miserables`: Characters in Les Misérables
+    - `sc_multiomics`: Single-cell multi-omics dataset from COVID-19 patients
+    - `track`: Track data from GEO GSE137105 for MYC gene
 
     Parameters
     ----------
@@ -47,6 +47,8 @@ def load_data(name, cache=True):
         return _load_cooking_oils(cache)
     elif name == "les_miserables":
         return _load_les_miserables(cache)
+    elif name == "track":
+        return _load_track(cache)
     else:
         raise NameError("Dataset not found")
 
@@ -151,3 +153,8 @@ def _load_les_miserables(cache=True):
         cache=cache,
     )
     return {"nodes": pd.read_csv(nodes), "links": pd.read_csv(links)}
+
+
+def _load_track(cache=True):
+    data = _cache_remote("track.parquet", cache=cache)
+    return pd.read_parquet(data)

{marsilea-0.4.3 → marsilea-0.4.5}/src/marsilea/plotter/__init__.py

@@ -23,6 +23,9 @@ __all__ = [
     "Chunk",
     "FixedChunk",
     "Area",
+    "Image",
+    "Emoji",
+    "Range",
 ]
 
 from ._seaborn import Bar, Box, Boxen, Violin, Point, Strip, Swarm
@@ -33,5 +36,6 @@ from .bio import SeqLogo
 from .mesh import Colors, ColorMesh, SizedMesh, MarkerMesh, TextMesh
 from .text import Labels, AnnoLabels, Title, Chunk, FixedChunk
 
-from ._images import Emoji, Image
+from .images import Emoji, Image
 from .area import Area
+from .range import Range

{marsilea-0.4.3 → marsilea-0.4.5}/src/marsilea/plotter/_seaborn.py

@@ -96,7 +96,7 @@ class _SeabornBase(StatsBase):
                 df["hue"] = hue
                 dfs.append(df)
 
-            pdata = pd.concat(dfs)
+            pdata = pd.concat(dfs).reset_index(drop=True)
             self.kws["hue"] = "hue"
             self.kws["hue_order"] = self.hue
             if self.get_orient() == "h":
@@ -123,7 +123,6 @@ class _SeabornBase(StatsBase):
             ax.invert_xaxis()
         # barplot(data=data, orient=orient, ax=ax, **self.kws)
         plotter = getattr(seaborn, self._seaborn_plot)
-
         plotter(data=pdata, orient=orient, ax=ax, **options)
         ax.set(xlabel=None, ylabel=None)
         leg = ax.get_legend()

marsilea-0.4.5/src/marsilea/plotter/range.py

@@ -0,0 +1,114 @@
+import pandas as pd
+from legendkit import cat_legend
+
+from marsilea.plotter.base import StatsBase, RenderSpec
+
+
+class Range(StatsBase):
+    """Range plot
+
+    The range plot shows the range between two categories.
+    The input data should be a DataFrame with two columns.
+
+    Parameters
+    ----------
+    data : array-like or DataFrame
+        The input data.
+    items : array-like, default: None
+        The names of the items.
+    marker : str, default: 'o'
+        The marker style.
+    markersize : float, default: 50
+        The size of the marker.
+    color1 : str, default: '#F75940'
+        The color of the first range.
+    color2 : str, default: '#3DC7BE'
+        The color of the second range.
+    edgecolor1 : str, default: 'black'
+        The edge color of the first range.
+    edgecolor2 : str, default: 'black'
+        The edge color of the second range.
+    edgewidth : float, default: 1
+        The width of the edge.
+    linecolor : str, default: 'black'
+        The color of the line.
+    linewidth : float, default: 1
+        The width of the line.
+    label : str, default: None
+        The label of the plot.
+
+    Examples
+    --------
+
+    .. plot::
+        :context: close-figs
+
+        >>> import marsilea as ma
+        >>> import numpy as np
+        >>> data = np.random.rand(10, 2)
+        >>> range_data = np.random.randint(1, 100, (10, 2))
+        >>> h = ma.Heatmap(data)
+        >>> h.add_left(ma.plotter.Range(range_data, items=["A", "B"]))
+        >>> h.render()
+
+
+    """
+
+    def __init__(self,
+                 data,
+                 items=None,
+                 marker='o',
+                 markersize=50,
+                 color1='#F75940',
+                 color2='#3DC7BE',
+                 edgecolor1='black',
+                 edgecolor2='black',
+                 edgewidth=1,
+                 linecolor='black',
+                 linewidth=1,
+                 label=None,
+                 ):
+        if isinstance(data, pd.DataFrame):
+            if items is None:
+                items = data.columns
+            data = data.to_numpy()
+        else:
+            data = data
+            if items is None:
+                items = [f"Item {i}" for i in range(data.shape[1])]
+        data = self.data_validator(data, target="2d")
+        self.set_data(data.T)
+        self.set_label(label)
+        self.items = items
+        self.marker = marker
+        self.markersize = markersize
+        self.color1 = color1
+        self.color2 = color2
+        self.edgecolor1 = edgecolor1
+        self.edgecolor2 = edgecolor2
+        self.edgewidth = edgewidth
+        self.linecolor = linecolor
+        self.linewidth = linewidth
+
+    def render_ax(self, spec: RenderSpec):
+        ax = spec.ax
+        data = spec.data.T
+
+        for ix, (r1, r2) in enumerate(data):
+            ix += .5
+            x, y = [ix, ix], [r1, r2]
+            if self.is_flank:
+                x, y = y, x
+            ax.scatter([x[0]], [y[0]], s=self.markersize, marker=self.marker, color=self.color1, edgecolor=self.edgecolor1, zorder=1)
+            ax.scatter([x[1]], [y[1]], s=self.markersize, marker=self.marker, color=self.color2, edgecolor=self.edgecolor2, zorder=1)
+            ax.plot(x, y, color=self.linecolor, linewidth=self.linewidth, zorder=0)
+
+        if self.is_flank:
+            ax.set_ylim(0, len(data))
+        else:
+            ax.set_xlim(0, len(data))
+        if self.side == "left":
+            ax.invert_xaxis()
+
+    def get_legends(self):
+        return [cat_legend(colors=[self.color1, self.color2], labels=self.items, title=self.label)]