marsilea 0.4.2__py3-none-any.whl → 0.4.4__py3-none-any.whl

marsilea/plotter/images.py

@@ -0,0 +1,293 @@
+# The implementation of Image in matplotlib may suffer from compatibility
+# issues across different rendering backend at different DPI. Currently
+# not a public API.
+from functools import partial
+from hashlib import sha256
+from numbers import Number
+from pathlib import Path
+
+import numpy as np
+from PIL import Image as PILImage
+from matplotlib.image import imread, BboxImage
+from matplotlib.transforms import Bbox
+from platformdirs import user_cache_dir
+
+from .base import RenderPlan
+
+
+def _cache_remote(url, cache=True):
+    try:
+        import requests
+    except ImportError:
+        raise ImportError("Required requests, try `pip install requests`.")
+    data_dir = Path(user_cache_dir(appname="Marsilea"))
+    data_dir.mkdir(exist_ok=True, parents=True)
+
+    hasher = sha256()
+    hasher.update(url.encode("utf-8"))
+    fname = hasher.hexdigest()
+
+    dest = data_dir / fname
+    if not (cache and dest.exists()):
+        r = requests.get(url, headers={"User-Agent": "Mozilla/5.0"})
+        r.raise_for_status()
+        with open(dest, "wb") as f:
+            f.write(r.content)
+
+    return dest
+
+
+class Image(RenderPlan):
+    """Plot static images
+
+    Parameters
+    ----------
+    images : array of image
+        You can input either path to the image, URL, or numpy array.
+    align : {"center", "top", "bottom", "left", "right"}, default: "center"
+        The alignment of the images.
+    scale : float, default: 1
+        The scale of the images.
+    spacing : float, default: 0.1
+        The spacing between images, a value between 0 and 1,
+        relative to the image container size.
+    resize : int or tuple, default: None
+        The size to resize the images.
+
+    Examples
+    --------
+
+    .. plot::
+        :context: close-figs
+
+        >>> import numpy as np
+        >>> import marsilea as ma
+        >>> c = ma.ZeroWidth(height=2)
+        >>> c.add_right(
+        ...     ma.plotter.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",
+        ...     ),
+        ...     pad=0.1,
+        ... )
+        >>> c.add_right(
+        ...     ma.plotter.Labels(["Python", "Rust", "JavaScript"], fontsize=20), pad=0.1
+        ... )
+        >>> c.render()
+
+    """
+
+    def __init__(
+        self,
+        images,
+        align="center",
+        scale=1,
+        spacing=0.1,
+        resize=None,
+    ):
+        self.images_mapper = {}
+
+        for i, img in enumerate(images):
+            if isinstance(img, str):
+                # Read from URL
+                if img.startswith("http") or img.startswith("https"):
+                    img = imread(_cache_remote(img))
+                else:
+                    # Read from string path
+                    img = imread(img)
+            # Read from Path
+            elif isinstance(img, Path):
+                img = imread(img)
+            else:
+                # Read from array interface
+                img = np.asarray(img)
+
+            self.images_mapper[i] = img
+
+        self.images_codes = np.asarray(list(self.images_mapper.keys()))
+
+        self.images = images
+        self.align = align
+        self.scale = scale
+        if not 0 <= spacing <= 1:
+            raise ValueError("spacing should be between 0 and 1")
+        self.spacing = spacing
+        if resize is not None:
+            if isinstance(resize, Number):
+                resize = (int(resize), int(resize))
+            for i, img in self.images_mapper.items():
+                self.images_mapper[i] = img.resize(resize, PILImage.Resampling.LANCZOS)
+        for i, img in self.images_mapper.items():
+            self.images_mapper[i] = np.asarray(img)
+        self.set_data(self.images_codes)
+
+    def _get_bbox_imges(
+        self, ax, imgs, scale=1, align="center", ax_height=None, ax_width=None
+    ):
+        locs = np.linspace(0, 1, len(imgs) + 1)
+        slot_size = locs[1] - locs[0]
+        locs = locs[:-1] + slot_size * self.spacing / 2
+
+        xmin, ymin = ax.transAxes.transform((0, 0))
+        xmax, ymax = ax.transAxes.transform((1, 1))
+
+        if ax_width is None or ax_width == 0:
+            ax_width = xmax - xmin
+        if ax_height is None or ax_height == 0:
+            ax_height = ymax - ymin
+
+        base_dpi = ax.get_figure().get_dpi()
+
+        bbox_images = []
+        imgaes_sizes = []
+
+        if self.is_body:
+            fit_width = ax_width / len(imgs) * (1 - self.spacing)
+            for loc, img in zip(locs, imgs):
+                height, width = img.shape[:2]
+                fit_height = height / width * fit_width
+
+                fit_scale_width = fit_width * scale
+                fit_scale_height = fit_height * scale
+
+                offset = (fit_width - fit_scale_width) / 2 / ax_width
+                loc += offset
+
+                if align == "top":
+                    loc_y = 1 - fit_scale_height / ax_height
+                elif align == "bottom":
+                    loc_y = 0
+                else:
+                    loc_y = 0.5 - fit_scale_height / 2 / ax_height
+
+                def img_bbox(renderer, loc, loc_y, width, height, base_dpi):
+                    factor = renderer.dpi / base_dpi
+                    x0, y0 = ax.transData.transform((loc, loc_y))
+                    return Bbox.from_bounds(x0, y0, width * factor, height * factor)
+
+                memorized_img_bbox = partial(
+                    img_bbox,
+                    loc=loc,
+                    loc_y=loc_y,
+                    width=fit_scale_width,
+                    height=fit_scale_height,
+                    base_dpi=base_dpi,
+                )
+
+                i1 = BboxImage(memorized_img_bbox, data=img)
+                bbox_images.append(i1)
+                imgaes_sizes.append(fit_scale_height)
+        else:
+            fit_height = ax_height / len(imgs) * (1 - self.spacing)
+            for loc, img in zip(locs, imgs[::-1]):
+                height, width = img.shape[:2]
+                fit_width = width / height * fit_height
+
+                fit_scale_width = fit_width * scale
+                fit_scale_height = fit_height * scale
+
+                offset = (fit_height - fit_scale_height) / 2 / ax_height
+                loc += offset
+
+                if align == "right":
+                    loc_x = 1 - fit_scale_width / ax_width
+                elif align == "left":
+                    loc_x = 0
+                else:
+                    loc_x = 0.5 - fit_scale_width / 2 / ax_width
+
+                def img_bbox(renderer, loc_x, loc, width, height, base_dpi):
+                    factor = renderer.dpi / base_dpi
+                    x0, y0 = ax.transData.transform((loc_x, loc))
+                    return Bbox.from_bounds(x0, y0, width * factor, height * factor)
+
+                memorized_img_bbox = partial(
+                    img_bbox,
+                    loc_x=loc_x,
+                    loc=loc,
+                    width=fit_scale_width,
+                    height=fit_scale_height,
+                    base_dpi=base_dpi,
+                )
+
+                i1 = BboxImage(memorized_img_bbox, data=img)
+                bbox_images.append(i1)
+                imgaes_sizes.append(fit_scale_width)
+
+        return bbox_images, max(imgaes_sizes)
+
+    def render_ax(self, spec):
+        ax = spec.ax
+        imgs = [self.images_mapper[i] for i in spec.data]
+        bbox_images, _ = self._get_bbox_imges(ax, imgs)
+        for i in bbox_images:
+            ax.add_artist(i)
+        ax.set_axis_off()
+
+    def get_canvas_size(
+        self, figure, main_height=None, main_width=None, **kwargs
+    ) -> float:
+        ax = figure.add_subplot(111)
+        imgs = [self.images_mapper[i] for i in self.images_codes]
+        _, size = self._get_bbox_imges(
+            ax, imgs, ax_width=main_width, ax_height=main_height
+        )
+        ax.remove()
+        return size
+
+
+# ======== EMOJI Plotter ========
+
+TWEMOJI_CDN = "https://cdn.jsdelivr.net/gh/twitter/twemoji/assets/72x72/"
+
+
+class Emoji(Image):
+    """Have fun with emoji images
+
+    The emoji images are from `twemoji <https://twemoji.twitter.com/>`_.
+
+    You can will all twemoji from `here <https://twemoji-cheatsheet.vercel.app/>`_
+
+    Parameters
+    ----------
+    codes : array of str
+        The emoji codes. You can input either unicode or short code.
+    lang : str, default: "en"
+        The language of the emoji.
+    scale : float, default: 1
+        The scale of the emoji.
+    spacing : float, default: 0.1
+        The spacing between emoji, a value between 0 and 1,
+        relative to the emoji container size.
+
+    Examples
+    --------
+
+    .. plot::
+
+        >>> import marsilea as ma
+        >>> c = ma.ZeroHeight(width=2)
+        >>> c.add_top(ma.plotter.Emoji("😆😆🤣😂😉😇🐍🦀🦄"))
+        >>> c.render()
+
+    """
+
+    def __init__(self, codes, lang="en", scale=1, spacing=0.1, **kwargs):
+        try:
+            import emoji
+        except ImportError:
+            raise ImportError("Required emoji, try `pip install emoji`.")
+
+        urls = []
+        for i in codes:
+            i = emoji.emojize(i, language=lang)
+            if not emoji.is_emoji(i):
+                raise ValueError(f"{i} is not a valid emoji")
+            c = f"{ord(i):X}".lower()
+            urls.append(f"{TWEMOJI_CDN}{c}.png")
+
+        super().__init__(urls, scale=scale, spacing=spacing, **kwargs)

marsilea/plotter/mesh.py

@@ -103,7 +103,7 @@ class ColorMesh(MeshBase):
 
         >>> import marsilea as ma
         >>> from marsilea.plotter import ColorMesh
-        >>> _, ax = plt.subplots(figsize=(5, .5))
+        >>> _, ax = plt.subplots(figsize=(5, 0.5))
         >>> ColorMesh(np.arange(10), cmap="Blues").render(ax)
 
     .. plot::
@@ -111,13 +111,13 @@ class ColorMesh(MeshBase):
 
         >>> data = np.random.randn(10, 8)
         >>> h = ma.Heatmap(data)
-        >>> h.hsplit(cut=[5])
+        >>> h.cut_rows(cut=[5])
         >>> h.add_dendrogram("left")
         >>> cmap1, cmap2 = "Purples", "Greens"
-        >>> colors1 = ColorMesh(np.arange(10)+1, cmap=cmap1, label=cmap1, annot=True)
-        >>> colors2 = ColorMesh(np.arange(10)+1, cmap=cmap2, label=cmap2)
-        >>> h.add_right(colors1, size=.2, pad=.05)
-        >>> h.add_right(colors2, size=.2, pad=.05)
+        >>> colors1 = ColorMesh(np.arange(10) + 1, cmap=cmap1, label=cmap1, annot=True)
+        >>> colors2 = ColorMesh(np.arange(10) + 1, cmap=cmap2, label=cmap2)
+        >>> h.add_right(colors1, size=0.2, pad=0.05)
+        >>> h.add_right(colors2, size=0.2, pad=0.05)
         >>> h.render()
 
 
@@ -280,7 +280,7 @@ class Colors(MeshBase):
 
         >>> import marsilea as ma
         >>> from marsilea.plotter import Colors
-        >>> _, ax = plt.subplots(figsize=(5, .5))
+        >>> _, ax = plt.subplots(figsize=(5, 0.5))
         >>> data = np.random.choice(["A", "B", "C"], 10)
         >>> Colors(data).render(ax)
 
@@ -288,10 +288,10 @@ class Colors(MeshBase):
         :context: close-figs
 
         >>> h = ma.Heatmap(np.random.randn(10, 8))
-        >>> h.hsplit(cut=[5])
+        >>> h.cut_rows(cut=[5])
         >>> h.add_dendrogram("left")
         >>> color = Colors(data, label="Colors")
-        >>> h.add_right(color, size=.2, pad=.05)
+        >>> h.add_right(color, size=0.2, pad=0.05)
         >>> h.render()
 
 
@@ -467,7 +467,7 @@ class SizedMesh(MeshBase):
 
         >>> import marsilea as ma
         >>> from marsilea.plotter import SizedMesh
-        >>> _, ax = plt.subplots(figsize=(5, .5))
+        >>> _, ax = plt.subplots(figsize=(5, 0.5))
         >>> size, color = np.random.rand(1, 10), np.random.rand(1, 10)
         >>> SizedMesh(size, color).render(ax)
 
@@ -475,10 +475,10 @@ class SizedMesh(MeshBase):
         :context: close-figs
 
         >>> h = ma.Heatmap(np.random.randn(10, 8))
-        >>> h.hsplit(cut=[5])
+        >>> h.cut_rows(cut=[5])
         >>> h.add_dendrogram("left")
         >>> mesh = SizedMesh(size, color, marker="*", label="SizedMesh")
-        >>> h.add_right(mesh, size=.2, pad=.05)
+        >>> h.add_right(mesh, size=0.2, pad=0.05)
         >>> h.render()
 
 
@@ -668,6 +668,8 @@ class MarkerMesh(MeshBase):
         See :mod:`matplotlib.markers`
     size : int
         The of marker in fontsize unit
+    frameon : bool
+        Whether to draw the border of the plot
     label : str
         The label of the plot, only show when added to the side plot
     label_loc : {'top', 'bottom', 'left', 'right'}
@@ -698,6 +700,7 @@ class MarkerMesh(MeshBase):
         color="black",
         marker="*",
         size=35,
+        frameon=False,
         label=None,
         label_loc=None,
         label_props=None,
@@ -706,9 +709,10 @@ class MarkerMesh(MeshBase):
         self.set_data(np.asarray(data))
         self.color = color
         self.marker = marker
+        self.marker_size = size
+        self.frameon = frameon
         self.set_label(label, label_loc, label_props)
         self.kwargs = kwargs
-        self.marker_size = size
 
     def get_legends(self):
         return CatLegend(
@@ -737,6 +741,8 @@ class MarkerMesh(MeshBase):
         ax.set_xlim(0, xticks[-1] + 0.5)
         ax.set_ylim(0, yticks[-1] + 0.5)
         ax.invert_yaxis()
+        if not self.frameon:
+            ax.set_axis_off()
 
 
 class TextMesh(MeshBase):
@@ -748,6 +754,8 @@ class TextMesh(MeshBase):
         The text to draw
     color : color
         The color of the text
+    frameon : bool
+        Whether to draw the border of the plot
     label : str
         The label of the plot, only show when added to the side plot
     label_loc : {'top', 'bottom', 'left', 'right'}
@@ -765,6 +773,7 @@ class TextMesh(MeshBase):
         self,
         texts,
         color="black",
+        frameon=False,
         label=None,
         label_loc=None,
         label_props=None,
@@ -772,6 +781,7 @@ class TextMesh(MeshBase):
     ):
         self.set_data(self.data_validator(texts))
         self.color = color
+        self.frameon = frameon
         self.set_label(label, label_loc, label_props)
         self.kwargs = kwargs
 
@@ -797,3 +807,5 @@ class TextMesh(MeshBase):
         ax.set_xlim(0, xticks[-1] + 0.5)
         ax.set_ylim(0, yticks[-1] + 0.5)
         ax.invert_yaxis()
+        if not self.frameon:
+            ax.set_axis_off()

marsilea/plotter/text.py

@@ -10,6 +10,7 @@ import warnings
 from dataclasses import dataclass
 from matplotlib.axes import Axes
 from matplotlib.colors import is_color_like
+from matplotlib.lines import Line2D
 from matplotlib.patches import Rectangle
 from matplotlib.text import Text
 from typing import List, Iterable
@@ -389,7 +390,7 @@ class _LabelBase(RenderPlan):
         ax.remove()
         return np.max(sizes) / figure.get_dpi()
 
-    def get_canvas_size(self, figure):
+    def get_canvas_size(self, figure, **kwargs):
         self.texts_size = self.silent_render(figure, expand=self.get_expand())
         return self.texts_size + self.padding / 72
 
@@ -545,7 +546,7 @@ class AnnoLabels(_LabelBase):
         p.update_params(self._user_params)
         return p
 
-    def get_canvas_size(self, figure):
+    def get_canvas_size(self, figure, **kwargs):
         expand = self.get_expand()
         canvas_size = self.silent_render(figure, expand)
         size = canvas_size + self.pointer_size
@@ -651,7 +652,7 @@ class Labels(_LabelBase):
         >>> import marsilea as ma
         >>> from marsilea.plotter import Labels
         >>> h = ma.Heatmap(np.random.randn(20, 20))
-        >>> h.add_right(Labels(labels, text_props={'color': colors}))
+        >>> h.add_right(Labels(labels, text_props={"color": colors}))
         >>> h.render()
 
     """
@@ -778,10 +779,10 @@ class Title(_LabelBase):
         >>> matrix = np.random.randn(15, 10)
         >>> h = ma.Heatmap(matrix)
         >>> for align in ["left", "right", "center"]:
-        ...     title = Title(f'Title align={align}', align=align)
+        ...     title = Title(f"Title align={align}", align=align)
         ...     h.add_top(title)
         >>> for align in ["top", "bottom", "center"]:
-        ...     title = Title(f'Title align={align}', align=align)
+        ...     title = Title(f"Title align={align}", align=align)
         ...     h.add_left(title)
         >>> h.render()
 
@@ -887,6 +888,7 @@ class _ChunkBase(_LabelBase):
         align=None,
         props=None,
         padding=2,
+        underline=False,
         bordercolor=None,
         borderwidth=None,
         borderstyle=None,
@@ -910,6 +912,7 @@ class _ChunkBase(_LabelBase):
             props = [props for _ in range(n)]
         self.props = props
 
+        self.underline = underline
         if is_color_like(bordercolor):
             bordercolor = [bordercolor for _ in range(n)]
         if bordercolor is not None:
@@ -924,6 +927,12 @@ class _ChunkBase(_LabelBase):
             borderstyle = [borderstyle for _ in range(n)]
         self.borderstyle = borderstyle
 
+        if self.underline:
+            if self.bordercolor is None:
+                self.bordercolor = np.asarray(["black" for _ in range(n)])
+            if self.borderwidth is None:
+                self.borderwidth = np.asarray([3 for _ in range(n)])
+
         self._draw_bg = (self.fill_colors is not None) or (self.bordercolor is not None)
         self.text_pad = 0
 
@@ -941,6 +950,13 @@ class _ChunkBase(_LabelBase):
         "bottom": 0,
     }
 
+    default_underline = {
+        "right": [(0, 0), (0, 1)],
+        "left": [(1, 1), (1, 0)],
+        "top": [(0, 1), (0, 0)],
+        "bottom": [(0, 1), (1, 1)],
+    }
+
     def get_alignment(self, ha, va, rotation):
         if rotation in {90, -90}:
             ha, va = va, ha  # swap the alignment
@@ -1005,16 +1021,27 @@ class _ChunkBase(_LabelBase):
             if self._draw_bg:
                 if bgcolor is None:
                     bgcolor = "white"
-                rect = Rectangle(
-                    (0, 0),
-                    1,
-                    1,
-                    facecolor=bgcolor,
-                    edgecolor=bc,
-                    linewidth=lw,
-                    linestyle=ls,
-                    transform=ax.transAxes,
-                )
+                if not self.underline:
+                    rect = Rectangle(
+                        (0, 0),
+                        1,
+                        1,
+                        facecolor=bgcolor,
+                        edgecolor=bc,
+                        linewidth=lw,
+                        linestyle=ls,
+                        transform=ax.transAxes,
+                    )
+                else:
+                    xdata, ydata = self.default_underline[self.side]
+                    rect = Line2D(
+                        xdata,
+                        ydata,
+                        color=bc,
+                        linewidth=lw,
+                        linestyle=ls,
+                        transform=ax.transAxes,
+                    )
                 ax.add_artist(rect)
                 fontdict.setdefault("color", self.get_text_color(bgcolor))
 
@@ -1069,10 +1096,10 @@ class Chunk(_ChunkBase):
         >>> from marsilea.plotter import Chunk
         >>> matrix = np.random.randn(20, 20)
         >>> h = ma.Heatmap(matrix)
-        >>> chunk = ['C1', 'C2', 'C3', 'C4']
+        >>> chunk = ["C1", "C2", "C3", "C4"]
         >>> labels = np.random.choice(chunk, size=20)
-        >>> h.hsplit(labels=labels, order=chunk)
-        >>> h.add_right(Chunk(chunk, bordercolor="gray"), pad=.1)
+        >>> h.group_rows(labels, order=chunk)
+        >>> h.add_right(Chunk(chunk, bordercolor="gray"), pad=0.1)
         >>> h.add_dendrogram("left")
         >>> h.render()
 
@@ -1086,6 +1113,7 @@ class Chunk(_ChunkBase):
         align=None,
         props=None,
         padding=8,
+        underline=False,
         bordercolor=None,
         borderwidth=None,
         borderstyle=None,
@@ -1100,6 +1128,7 @@ class Chunk(_ChunkBase):
             align=align,
             props=props,
             padding=padding,
+            underline=underline,
             bordercolor=bordercolor,
             borderwidth=borderwidth,
             borderstyle=borderstyle,
@@ -1175,10 +1204,10 @@ class FixedChunk(_ChunkBase):
         >>> from marsilea.plotter import FixedChunk
         >>> matrix = np.random.randn(20, 20)
         >>> h = ma.Heatmap(matrix)
-        >>> chunk = ['C1', 'C2', 'C3', 'C4']
+        >>> chunk = ["C1", "C2", "C3", "C4"]
         >>> labels = np.random.choice(chunk, size=20)
-        >>> h.hsplit(labels=labels, order=chunk)
-        >>> h.add_right(FixedChunk(chunk, bordercolor="gray"), pad=.1)
+        >>> h.group_rows(labels, order=chunk)
+        >>> h.add_right(FixedChunk(chunk, bordercolor="gray"), pad=0.1)
         >>> h.add_dendrogram("left")
         >>> h.render()
 
@@ -1188,12 +1217,18 @@ class FixedChunk(_ChunkBase):
         :context: close-figs
 
         >>> h = ma.Heatmap(matrix)
-        >>> chunk = ['C1', 'C2-1', 'C2-2', 'C4']
+        >>> chunk = ["C1", "C2-1", "C2-2", "C4"]
         >>> labels = np.random.choice(chunk, size=20)
-        >>> h.hsplit(labels=labels, order=chunk)
-        >>> h.add_right(FixedChunk(chunk, bordercolor="gray"), pad=.1)
-        >>> h.add_right(FixedChunk(['C1', 'C2', 'C3'], fill_colors="red",
-        ...                        ratio=[1, 2, 1], ), pad=.1)
+        >>> h.group_rows(labels, order=chunk)
+        >>> h.add_right(FixedChunk(chunk, bordercolor="gray"), pad=0.1)
+        >>> h.add_right(
+        ...     FixedChunk(
+        ...         ["C1", "C2", "C3"],
+        ...         fill_colors="red",
+        ...         ratio=[1, 2, 1],
+        ...     ),
+        ...     pad=0.1,
+        ... )
         >>> h.render()
 
 
@@ -1208,6 +1243,7 @@ class FixedChunk(_ChunkBase):
         ratio=None,
         props=None,
         padding=8,
+        underline=False,
         bordercolor=None,
         borderwidth=None,
         borderstyle=None,
@@ -1219,12 +1255,13 @@ class FixedChunk(_ChunkBase):
         super().__init__(
             texts,
             fill_colors,
-            align,
-            props,
-            padding,
-            bordercolor,
-            borderwidth,
-            borderstyle,
+            align=align,
+            props=props,
+            padding=padding,
+            underline=underline,
+            bordercolor=bordercolor,
+            borderwidth=borderwidth,
+            borderstyle=borderstyle,
             **options,
         )
         if ratio is not None:

marsilea/utils.py

@@ -2,7 +2,6 @@ import matplotlib as mpl
 import numpy as np
 from itertools import tee, islice
 from matplotlib import colors as mcolors
-from matplotlib.colors import Colormap
 from uuid import uuid4
 
 ECHARTS16 = [
@@ -70,7 +69,7 @@ def relative_luminance(color):
 
 def get_colormap(cmap):
     try:
-        return mpl.cm.ColormapRegistry.get_cmap(cmap)
+        return mpl.colormaps.get_cmap(cmap)
     except AttributeError:
         try:
             return mpl.colormaps.get(cmap)