Add pre-commit hooks

Marsilea-viz · Sep 8, 2024 · a318de5 · a318de5
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diff --git a/docs/examples/Gallery/plot_oil_well.py b/docs/examples/Gallery/plot_oil_well.py
@@ -98,7 +98,7 @@
     "150-199 °C (Light saute)",
     "<150 °C (Dressings)",
 ]
-cb.hsplit(labels=oils["cooking conditions"], order=order)
+cb.group_rows(oils["cooking conditions"], order=order)
 cb.add_left(conditions, pad=0.1)
 cb.add_dendrogram(
     "left", add_meta=False, colors=colors, linewidth=1.5, size=0.5, pad=0.02

diff --git a/docs/examples/Gallery/plot_pbmc3k.py b/docs/examples/Gallery/plot_pbmc3k.py
@@ -76,7 +76,7 @@
 h.add_left(cell_types)
 h.add_bottom(gene_names)
 
-h.hsplit(labels=cell_cat, order=["Lymphoid", "Myeloid"])
+h.group_rows(cell_cat, order=["Lymphoid", "Myeloid"])
 h.add_left(mp.Chunk(["Lymphoid", "Myeloid"], ["#33A6B8", "#B481BB"]), pad=0.05)
 h.add_dendrogram("left", colors=["#33A6B8", "#B481BB"])
 h.add_dendrogram("bottom")

diff --git a/docs/examples/Gallery/plot_sc_multiomics.py b/docs/examples/Gallery/plot_sc_multiomics.py
@@ -58,7 +58,7 @@
             "title": "% expression in group",
         },
     )
-    gene_profile.hsplit(labels=lineage_cells, order=lineage)
+    gene_profile.group_rows(lineage_cells, order=lineage)
     gene_profile.add_left(ma.plotter.Chunk(lineage, lineage_colors, padding=10))
     gene_profile.add_dendrogram(
         "left",
@@ -103,7 +103,7 @@
             "title": "% expression in group",
         },
     )
-    protein_profile.hsplit(labels=lineage_cells, order=lineage)
+    protein_profile.group_rows(lineage_cells, order=lineage)
     protein_profile.add_bottom(
         ma.plotter.Labels(marker_names, color="#E36414", align="bottom", padding=10)
     )

diff --git a/docs/examples/Gallery/plot_tiobe_index.py b/docs/examples/Gallery/plot_tiobe_index.py
@@ -27,8 +27,18 @@
 # ---------
 
 data = {
-    "Programming Language": ["Python", "C++", "C", "Java", "C#", "JavaScript",
-                             "Go", "Visual Basic", "Fortran", "SQL"],
+    "Programming Language": [
+        "Python",
+        "C++",
+        "C",
+        "Java",
+        "C#",
+        "JavaScript",
+        "Go",
+        "Visual Basic",
+        "Fortran",
+        "SQL",
+    ],
     "Ratings": [16.12, 10.34, 9.48, 8.59, 6.72, 3.79, 2.19, 2.08, 2.05, 2.04],
 }
 data = pd.DataFrame(data).set_index("Programming Language")
@@ -50,8 +60,10 @@
 # Plot
 c = ma.ZeroWidth(5)
 c.add_right(mp.Image([images[lang] for lang in data.index]))
-c.add_left(mp.Labels(data.index, fontweight=600), pad=.1)
-c.add_right(mp.Numbers(data['Ratings'], color="#009FBD", label="Rating"), pad=.1)
-c.add_title("https://www.tiobe.com/tiobe-index/", align="left", fontsize=10, fontstyle="italic")
+c.add_left(mp.Labels(data.index, fontweight=600), pad=0.1)
+c.add_right(mp.Numbers(data["Ratings"], color="#009FBD", label="Rating"), pad=0.1)
+c.add_title(
+    "https://www.tiobe.com/tiobe-index/", align="left", fontsize=10, fontstyle="italic"
+)
 c.add_title("TIOBE Index July 2024", align="left", fontweight=600)
 c.render()
diff --git a/docs/examples/Gallery/plot_tracks.py b/docs/examples/Gallery/plot_tracks.py
@@ -2,6 +2,7 @@
 Track Plot
 ==========
 """
+
 import marsilea as ma
 import marsilea.plotter as mp
 
@@ -42,8 +43,14 @@
     name = f"{cond}{enz}"
     color = colors[enz]
     canvas.add_bottom(
-        mp.Area(track, color=color, add_outline=False, alpha=1,
-                label=cond, label_loc="right"),
+        mp.Area(
+            track,
+            color=color,
+            add_outline=False,
+            alpha=1,
+            label=cond,
+            label_loc="right",
+        ),
         size=TRACK_HEIGHT,
         pad=TRACK_PAD,
         name=name,

diff --git a/docs/examples/Plotters/plot_chunk.py b/docs/examples/Plotters/plot_chunk.py
@@ -14,7 +14,7 @@
 h = ma.Heatmap(matrix)
 chunk = ["C1", "C2", "C3", "C4"]
 labels = np.random.choice(chunk, size=20)
-h.hsplit(labels=labels, order=chunk)
+h.group_rows(labels, order=chunk)
 h.add_right(Chunk(chunk, bordercolor="gray"), pad=0.1)
 h.add_dendrogram("left")
 h.render()
diff --git a/docs/examples/Plotters/plot_emoji.py b/docs/examples/Plotters/plot_emoji.py
@@ -8,11 +8,10 @@
 
 # %%
 
-from marsilea.plotter import Emoji
-
 # %%
-import numpy as np
 import matplotlib.pyplot as plt
 
+from marsilea.plotter import Emoji
+
 _, ax = plt.subplots()
 Emoji("😆😆🤣😂😉😇🐍🦀🦄").render(ax)
diff --git a/docs/examples/Plotters/plot_fixed_chunk.py b/docs/examples/Plotters/plot_fixed_chunk.py
@@ -15,7 +15,7 @@
 h = ma.Heatmap(matrix)
 chunk = ["C1", "C2-1", "C2-2", "C4"]
 labels = np.random.choice(chunk, size=20)
-h.hsplit(labels=labels, order=chunk)
+h.group_rows(labels, order=chunk)
 h.add_right(FixedChunk(chunk, bordercolor="gray"), pad=0.1)
 h.add_right(
     FixedChunk(

diff --git a/docs/examples/Plotters/plot_image.py b/docs/examples/Plotters/plot_image.py
@@ -8,15 +8,17 @@
 
 # %%
 
-from marsilea.plotter import Image
-
 # %%
-import numpy as np
 import matplotlib.pyplot as plt
 
+from marsilea.plotter import Image
+
 _, ax = plt.subplots()
-Image([
-    "https://www.iconfinder.com/icons/4375050/download/png/512",
-    "https://www.iconfinder.com/icons/8666426/download/png/512",
-    "https://www.iconfinder.com/icons/652581/download/png/512"
-], align="right").render(ax)
+Image(
+    [
+        "https://www.iconfinder.com/icons/4375050/download/png/512",
+        "https://www.iconfinder.com/icons/8666426/download/png/512",
+        "https://www.iconfinder.com/icons/652581/download/png/512",
+    ],
+    align="right",
+).render(ax)
diff --git a/docs/examples/Plotters/plot_labels.py b/docs/examples/Plotters/plot_labels.py
@@ -15,6 +15,6 @@
 
 _, ax = plt.subplots(figsize=(0.5, 6))
 data = np.random.randint(0, 10, 30)
-l = Labels(data)
-l.set_side("right")
-l.render(ax)
+labels = Labels(data)
+labels.set_side("right")
+labels.render(ax)
diff --git a/docs/how_to/legends/plot_custom_legend.py b/docs/how_to/legends/plot_custom_legend.py
@@ -10,15 +10,21 @@
 
 # %%
 import numpy as np
+
 import marsilea as ma
-from marsilea.plotter import ColorMesh, Colors
 
 data = np.random.randint(0, 10, (10, 10))
 
 
 # %%
 from legendkit import cat_legend
-def my_legend(): return cat_legend(labels=["my super legend"], colors=["lightblue"], title="My Legend")
+
+
+def my_legend():
+    return cat_legend(
+        labels=["my super legend"], colors=["lightblue"], title="My Legend"
+    )
+
 
 h = ma.Heatmap(data, width=3, height=3)
 h.custom_legend(my_legend)

diff --git a/docs/source/api/index.rst b/docs/source/api/index.rst
@@ -9,124 +9,147 @@ Declarative API Cheat Sheet
 
 .. list-table::
     :header-rows: 1
+    :widths: 10 50 50
 
     * - Operator
-      - Description
+      - Showcase
       - Example
 
-    * - :meth:`~marsilea.base.WhiteBoard.add_layer`
-      - Add a plotter to main canvas.
+
+    * - | :meth:`~marsilea.base.WhiteBoard.add_layer`
+        | Add a plotter to main canvas.
+      - .. image:: ../img/api_add_layer.png
       - .. code-block:: python
 
             wb.add_layer(ColorMesh(data))
 
-    * - :meth:`~marsilea.base.WhiteBoard.add_left`
-      - Add to the **left-side** of main canvas.
+    * - | :meth:`~marsilea.base.WhiteBoard.add_left`
+        | Add to the **left-side** of main canvas.
+      - .. image:: ../img/api_add_left.png
       - .. code-block:: python
 
             wb.add_left(Numbers(data),
                         size=1, pad=.1,
                         name='left-plot')
 
-    * - :meth:`~marsilea.base.WhiteBoard.add_right`
-      - Add a plotter to the **right-side** of main canvas.
+    * - | :meth:`~marsilea.base.WhiteBoard.add_right`
+        | Add a plotter to the **right-side** of main canvas.
+      - .. image:: ../img/api_add_right.png
       - .. code-block:: python
 
             wb.add_right(Numbers(data))
 
-    * - :meth:`~marsilea.base.WhiteBoard.add_top`
-      - Add a plotter to the **top-side** of main canvas.
+    * - | :meth:`~marsilea.base.WhiteBoard.add_top`
+        | Add a plotter to the **top-side** of main canvas.
+      - .. image:: ../img/api_add_top.png
       - .. code-block:: python
 
             wb.add_top(Numbers(data))
 
-    * - :meth:`~marsilea.base.WhiteBoard.add_bottom`
-      - Add a plotter to the **bottom-side** of main canvas.
+    * - | :meth:`~marsilea.base.WhiteBoard.add_bottom`
+        | Add a plotter to the **bottom-side** of main canvas.
+      - .. image:: ../img/api_add_bottom.png
       - .. code-block:: python
 
             wb.add_bottom(Numbers(data))
 
-    * - :meth:`~marsilea.base.WhiteBoard.add_title`
-      - Add titles to the plot.
+    * - | :meth:`~marsilea.base.WhiteBoard.add_title`
+        | Add titles to the plot.
+      - .. image:: ../img/api_add_title.png
       - .. code-block:: python
 
-            wb.add_title(top='Top Title', bottom='Bottom Title'
-                         left='Left Title', right='Right Title')
+            wb.add_title(top='Top', bottom='Bottom'
+                         left='Left', right='Right')
 
-    * - :meth:`~marsilea.base.ClusterBoard.add_dendrogram`
-      - Add a dendrogram to the plot, only available to ClusterBoard.
+    * - | :meth:`~marsilea.base.ClusterBoard.add_dendrogram`
+        | Add a dendrogram to the plot, only available to ClusterBoard.
+      - .. image:: ../img/api_add_dendrogram.png
       - .. code-block:: python
 
-            cb.add_dendrogram("left", data)
+            cb.add_dendrogram("right")
 
-    * - :meth:`~marsilea.base.ClusterBoard.group_cols`
-      - Split the main canvas horizontally, only available to ClusterBoard.
+    * - | :meth:`~marsilea.base.ClusterBoard.group_cols`
+        | Split the main canvas vertically by labeling columns, only available to ClusterBoard.
+      - .. image:: ../img/api_group_cols.png
       - .. code-block:: python
 
-            cb.group_cols(labels=[1, 1, 2, 2], order=[2, 1])
+            cb.group_cols(list("11223"))
 
-    * - :meth:`~marsilea.base.ClusterBoard.group_rows`
-      - Split the main canvas vertically, only available to ClusterBoard.
+    * - | :meth:`~marsilea.base.ClusterBoard.group_rows`
+        | Split the main canvas horizontally by labeling rows, only available to ClusterBoard.
+      - .. image:: ../img/api_group_rows.png
       - .. code-block:: python
 
-            cb.group_rows(labels=[1, 1, 2, 2], order=[2, 1])
+            cb.group_rows(list("11223"))
 
-    * - :meth:`~marsilea.base.ClusterBoard.cut_cols`
-      - Split the main canvas horizontally, only available to ClusterBoard.
+    * - | :meth:`~marsilea.base.ClusterBoard.cut_cols`
+        | Split the main canvas vertically by positions, only available to ClusterBoard.
+      - .. image:: ../img/api_cut_cols.png
       - .. code-block:: python
 
-            cb.cut_cols([5])
+            cb.cut_cols([2, 4])
 
-    * - :meth:`~marsilea.base.ClusterBoard.cut_rows`
-      - Split the main canvas vertically, only available to ClusterBoard.
+    * - | :meth:`~marsilea.base.ClusterBoard.cut_rows`
+        | Split the main canvas horizontally by positions, only available to ClusterBoard.
+      - .. image:: ../img/api_cut_rows.png
       - .. code-block:: python
 
-            cb.cut_rows([5])
+            cb.cut_rows([2, 4])
 
-    * - :meth:`~marsilea.base.LegendMaker.add_legends`
-      - Add legends to the plots.
+    * - | :meth:`~marsilea.base.LegendMaker.add_legends`
+        | Add legends to the plots.
+      - .. image:: ../img/api_add_legends.png
       - .. code-block:: python
 
             wb.add_legends()
 
-    * - :meth:`~marsilea.base.WhiteBoard.add_canvas`
-      - Add a plotter to a chosen side of main plot.
+    * - | :meth:`~marsilea.base.WhiteBoard.add_canvas`
+        | Add a empty canvas to a chosen side of main plot.
+      - .. image:: ../img/api_add_canvas.png
       - .. code-block:: python
 
-            wb.add_canvas("right", Numbers(data))
+            wb.add_canvas("right")
 
-    * - :meth:`~marsilea.base.WhiteBoard.add_pad`
-      - Add white space between plot.
+    * - | :meth:`~marsilea.base.WhiteBoard.add_pad`
+        | Add white space between plot.
+      - ---
       - .. code-block:: python
 
             wb.add_pad("right", 1)
 
-    * - :meth:`~marsilea.base.WhiteBoard.set_margin`
-      - Add white space surrounding the figure.
+    * - | :meth:`~marsilea.base.WhiteBoard.set_margin`
+        | Add white space surrounding the figure.
+      - ---
       - .. code-block:: python
 
             wb.set_margin(1)
 
-    * - :meth:`~marsilea.base.WhiteBoard.render`
-      - Render the plot.
+
+    * - | :meth:`~marsilea.base.WhiteBoard.render`
+        | Render the plot.
+      - ---
       - .. code-block:: python
 
             wb.render()
 
-    * - :meth:`~marsilea.base.WhiteBoard.save`
-      - Save the plot to a file.
+
+    * - | :meth:`~marsilea.base.WhiteBoard.save`
+        | Save the plot to a file.
+      - ---
       - .. code-block:: python
 
             wb.save("output.png", dpi=300)
 
-    * - :code:`+`
-      - Two canvas side by side, number will be added as white space
+    * - | :code:`+`
+        | Two canvas side by side, number will be added as white space
+      - .. image:: ../img/api_concatenate_plus.png
       - .. code-block:: python
 
             (wb1 + 1 + wb2).render()
 
-    * - :code:`/`
-      - Two canvas top and bottom, number will be added as white space
+    * - | :code:`/`
+        | Two canvas top and bottom, number will be added as white space
+      - .. image:: ../img/api_concatenate_divide.png
       - .. code-block:: python
 
             (wb1 / 1 / wb2).render()

diff --git a/docs/source/tutorial/axes-level.rst b/docs/source/tutorial/axes-level.rst
@@ -60,7 +60,7 @@ to retrieve the named axes.
     :context: close-figs
 
     >>> h = ma.Heatmap(data, linewidth=1)
-    >>> h.hsplit(cut=[5])
+    >>> h.cut_rows(cut=[5])
     >>> bar = ma.plotter.Numbers(np.arange(20))
     >>> h.add_right(bar, name="My Bar")
     >>> h.render()