marsilea 0.4.2__py3-none-any.whl → 0.4.3__py3-none-any.whl

oncoprinter/core.py

@@ -0,0 +1,360 @@
+import warnings
+from collections import Counter
+from copy import deepcopy
+from dataclasses import dataclass
+from itertools import count
+from typing import Any
+
+import numpy as np
+import pandas as pd
+from marsilea import ClusterBoard
+from marsilea.layers import LayersMesh, FrameRect, Piece
+from marsilea.plotter import Labels, StackBar, Numbers, ColorMesh
+from marsilea.utils import get_canvas_size_by_data
+
+from .preset import SHAPE_BANK, MATCH_POOL, Alteration
+
+
+def guess_alteration(event: str):
+    for alt, rule in MATCH_POOL.items():
+        if rule.is_match(event):
+            return alt
+    return Alteration.OTHER
+
+
+@dataclass(repr=False)
+class LayerData:
+    matrix: np.ndarray
+    piece: Piece
+    color: Any
+    event: Any
+
+    def __repr__(self):
+        return f"{self.piece.label} ({self.color})"
+
+
+class GenomicData:
+    """Handle class for genomics data
+
+    Parameters
+    ----------
+    data : pd.DataFrame
+        Each column is:
+            1) Sample ID
+            2) Track name
+            3) Alteration
+    samples_order : list, optional
+        The order of samples, by default None
+    tracks_order : list, optional
+        The order of tracks, by default None
+    custom_pieces : dict, optional
+        Custom pieces for each alteration, by default None
+
+    """
+
+    def __repr__(self):
+        ntrack, nsample = self.shape
+        return (
+            f"{ntrack} Tracks, {nsample} Samples with "
+            f"{len(self.events)} Alterations"
+        )
+
+    def __init__(
+        self,
+        data,
+        samples_order=None,
+        tracks_order=None,
+        custom_pieces=None,
+    ):
+        self.data = data.copy()
+        self.data.columns = ["sample", "track", "event"]
+
+        if samples_order is None:
+            samples_order = self.data["sample"].unique()
+
+        self.samples = samples_order
+        self._patients_ix = dict(zip(samples_order, count(0, 1)))
+
+        if tracks_order is None:
+            tracks_order = self.data["track"].unique()
+        self.tracks = tracks_order
+        self._tracks_ix = dict(zip(tracks_order, count(0, 1)))
+
+        self._shape = (len(self.tracks), len(self.samples))
+
+        if custom_pieces is None:
+            custom_pieces = {}
+        self.custom_pieces = custom_pieces
+
+        self._process_alterations()
+
+        layers = {}
+        for e in self.events:
+            layers[e] = np.zeros(self._shape, dtype=bool)
+
+        for _, row in self.data.iterrows():
+            patient, track, event = row
+            row_ix = self._tracks_ix[track]
+            col_ix = self._patients_ix[patient]
+            layers[event][row_ix, col_ix] = True
+
+        self.layers = layers
+
+    def _process_alterations(self):
+        events_alt = dict()
+        custom_events = list(self.custom_pieces.keys())
+        raw_events = self.data["event"].unique()
+
+        unknown_alterations = []
+        for e in raw_events:
+            alt = guess_alteration(e)
+            if alt == Alteration.OTHER:
+                alt = e
+                if e not in custom_events:
+                    unknown_alterations.append(e)
+            events_alt[e] = alt
+        self.data["event"] = [events_alt[e] for e in self.data["event"]]
+        self.events = self.data["event"].unique()
+        if len(unknown_alterations) > 0:
+            msg = (
+                f"Found unknown alterations: {unknown_alterations}, "
+                f"please specify a piece for this alteration."
+            )
+            warnings.warn(msg)
+
+    @property
+    def shape(self):
+        return self._shape
+
+    def get_layers_data(self, background_color="#BEBEBE"):
+        # explicitly make copy
+        bg_pieces = deepcopy(SHAPE_BANK[Alteration.BACKGROUND])
+        bg_pieces.background_color = background_color
+
+        # Add background layer
+        layers_data = [
+            LayerData(
+                np.ones(self._shape), bg_pieces, background_color, Alteration.BACKGROUND
+            )
+        ]
+        for alt in self.events:
+            layer = self.layers[alt]
+            if not isinstance(alt, Alteration):
+                piece = self.custom_pieces.get(alt)
+                if piece is None:
+                    # The default style for OTHER
+                    piece = FrameRect(color="pink", label=alt)
+                else:
+                    piece = deepcopy(piece)
+            else:
+                piece = deepcopy(SHAPE_BANK[alt])
+            color = piece.color
+            piece.background_color = background_color
+
+            layers_data.append(LayerData(layer, piece, color, alt))
+
+        return layers_data
+
+    def get_track_mutation_rate(self):
+        gb = self.data.groupby("track", sort=False, observed=True)
+        ts = {}
+        for track, df in gb:
+            ts[track] = len(df["sample"].unique())
+        counts = np.array([ts[t] for t in self.tracks])
+        return counts / len(self.samples)
+
+    def get_track_mutation_types(self):
+        gb = self.data.groupby("track", sort=False, observed=True)
+        cs = {}
+        for track, df in gb:
+            cs[track] = Counter(df["event"])
+        return pd.DataFrame(cs).fillna(0.0)
+
+    def get_sample_mutation_types(self):
+        gb = self.data.groupby("sample", sort=False, observed=True)
+        cs = {}
+        for track, df in gb:
+            cs[track] = Counter(df["event"])
+        return pd.DataFrame(cs).fillna(0.0)
+
+
+class OncoPrint(ClusterBoard):
+    """OncoPrint plot
+
+    The oncoprint plot is a visualization for genomics data in cancer research.
+    It's first introduced by the cBioPortal project.
+    See https://www.cbioportal.org/oncoprinter for more details.
+
+    To use this class, import from oncoprinter
+
+        >>> from oncoprinter import OncoPrint
+
+    Parameters
+    ----------
+    genomic_data : pd.DataFrame
+        Genomics data, each column is:
+            1) Sample ID
+            2) Track name
+            3) Alteration
+
+    patients_order : list, optional
+        The order of samples, by default None
+    tracks_order : list, optional
+        The order of tracks, by default None
+    pieces : dict, optional
+        Custom pieces for each alteration, by default None
+        See :class:`Piece <marsilea.layers.Piece>` for details
+    background_color : str, optional, default: "#BEBEBE"
+        The background color
+    shrink : tuple, optional, default: (0.8, 0.8)
+        The shrink ratio for each layer
+    width, height : float, optional
+        The size in inches to define the size of main canvas
+    aspect : float, optional, default: 2.5
+        The aspect ratio of the main canvas
+    legend_kws : dict, optional
+        The options for legend, by default None
+        See :class:`cat_legend <legendkit.cat_legend>` for details
+    name : str, optional
+        The name of this OncoPrint
+    add_tracks_names : str, optional, default: "left"
+        The position to add tracks names
+        If None, will not add tracks names
+    add_samples_names : str, optional, default: "bottom"
+        The position to add samples names
+        If None, will not add samples names
+    add_mut_perc : str, optional, default: "right"
+        The position to add mutation percentage
+        If None, will not add mutation percentage
+    add_tracks_counts : str, optional, default: "right"
+        The position to add tracks mutation counts
+        If None, will not add tracks mutation counts
+    add_mut_counts : str, optional, default: "top"
+        The position to add mutation counts
+        If None, will not add mutation counts
+    add_tracks_counts_size : float, optional, default: 0.2
+        The size of tracks mutation counts
+    add_tracks_counts_pad : float, optional, default: 0
+        The padding of tracks mutation counts
+    add_mut_counts_size : float, optional, default: 0.2
+        The size of mutation counts
+    add_mut_counts_pad : float, optional, default: 0.1
+        The padding of mutation counts
+
+    """
+
+    def __init__(
+        self,
+        genomic_data=None,
+        patients_order=None,
+        tracks_order=None,
+        pieces=None,
+        background_color="#BEBEBE",
+        shrink=(0.8, 0.8),
+        width=None,
+        height=None,
+        aspect=2.5,
+        legend_kws=None,
+        name=None,
+        add_tracks_names="left",
+        add_samples_names="bottom",
+        add_mut_perc="right",
+        add_tracks_counts="right",
+        add_mut_counts="top",
+        add_tracks_counts_size=0.2,
+        add_tracks_counts_pad=0,
+        add_mut_counts_size=0.2,
+        add_mut_counts_pad=0.1,
+    ):
+        data = GenomicData(
+            genomic_data,
+            samples_order=patients_order,
+            tracks_order=tracks_order,
+            custom_pieces=pieces,
+        )
+        self.genomic_data = data
+        width, height = get_canvas_size_by_data(
+            data.shape, width=width, height=height, scale=0.2, aspect=aspect
+        )
+
+        self.canvas = super().__init__(
+            name=name, cluster_data=np.zeros(data.shape), width=width, height=height
+        )
+
+        legend_options = dict(title="Alterations", handleheight=aspect, handlelength=1)
+        legend_kws = {} if legend_kws is None else legend_kws
+        legend_options.update(legend_kws)
+
+        layers, pieces, colors_mapper = [], [], {}
+        for layer in data.get_layers_data(background_color):
+            layers.append(layer.matrix)
+            pieces.append(layer.piece)
+            colors_mapper[layer.event] = layer.color
+        mesh = LayersMesh(
+            layers=layers, pieces=pieces, shrink=shrink, legend_kws=legend_options
+        )
+        self.add_layer(mesh)
+
+        if add_tracks_names:
+            self.add_plot(add_tracks_names, Labels(data.tracks))
+
+        # Add other statistics
+        track_mut_rate = data.get_track_mutation_rate()
+        # Convert to percentage string
+        if add_mut_perc:
+            rates = [_format_percentage(t) for t in track_mut_rate]
+            self.add_plot(add_mut_perc, Labels(rates))
+        if add_samples_names:
+            self.add_plot(add_samples_names, Labels(data.samples))
+
+        if add_tracks_counts:
+            track_counter = data.get_track_mutation_types()
+            colors = [colors_mapper[e] for e in track_counter.index]
+            track_bar = StackBar(track_counter, colors=colors, show_value=False)
+            self.add_plot(
+                add_tracks_counts,
+                track_bar,
+                legend=False,
+                size=add_tracks_counts_size,
+                pad=add_tracks_counts_pad,
+            )
+
+        if add_mut_counts:
+            patients_counter = data.get_sample_mutation_types()
+            colors = [colors_mapper[e] for e in patients_counter.index]
+            patients_bar = StackBar(patients_counter, colors=colors, show_value=False)
+            self.add_plot(
+                add_mut_counts,
+                patients_bar,
+                legend=False,
+                size=add_mut_counts_size,
+                pad=add_mut_counts_pad,
+            )
+        self.add_legends()
+
+    clinical_plots = {
+        "bar": Numbers,
+        "stack_bar": StackBar,
+    }
+
+    def add_clinical_data(self, data, plot="bar", size=None, pad=0.1, **kwargs):
+        data = data.loc[self.samples_order]
+        plotter = self.clinical_plots[plot]
+        self.add_bottom(plotter(data, **kwargs), size=size, pad=pad)
+
+    def add_heatmap_data(self, data, size=0.2, pad=0.1, **kwargs):
+        data = data.loc[self.samples_order]
+        options = {"cmap": "Blues", "label_loc": "left", **kwargs}
+        self.add_bottom(ColorMesh(data, **options), size=size, pad=pad)
+
+    @property
+    def samples_order(self):
+        return self.genomic_data.samples
+
+    @property
+    def tracks_order(self):
+        return self.genomic_data.tracks
+
+
+def _format_percentage(t):
+    return f"{float(t) * 100:.2f}".rstrip("0").rstrip(".") + "%"

oncoprinter/preset.py

@@ -0,0 +1,258 @@
+from dataclasses import dataclass, field
+from enum import Enum, auto
+from typing import List
+
+import marsilea.layers as mlayers
+import numpy as np
+from matplotlib.collections import PatchCollection
+from matplotlib.patches import Rectangle
+
+# The preset follows the style of cBioPortal as much as possible
+# https://github.com/cBioPortal/cbioportal-frontend/blob/master/src/shared/components/oncoprint/geneticrules.ts
+MUT_COLOR_MISSENSE = "#008000"
+MUT_COLOR_MISSENSE_PASSENGER = "#53D400"
+MUT_COLOR_INFRAME = "#993404"
+MUT_COLOR_INFRAME_PASSENGER = "#a68028"
+MUT_COLOR_TRUNC = "#000000"
+MUT_COLOR_TRUNC_PASSENGER = "#708090"
+MUT_COLOR_SPLICE = "#e5802b"
+MUT_COLOR_SPLICE_PASSENGER = "#f0b87b"
+MUT_COLOR_PROMOTER = "#00B7CE"
+MUT_COLOR_OTHER = "#cf58bc"
+
+MUT_DRIVER = "#000000"
+MUT_VUS = "#696969"
+MUT_COLOR_GERMLINE = "#FFFFFF"
+
+MRNA_COLOR_HIGH = "#ff9999"
+MRNA_COLOR_LOW = "#6699cc"
+
+PROT_COLOR_HIGH = "#ff3df8"
+PROT_COLOR_LOW = "#00E1FF"
+
+CNA_COLOR_AMP = "#ff0000"
+CNA_COLOR_GAIN = "#ffb6c1"
+CNA_COLOR_HETLOSS = "#8fd8d8"
+CNA_COLOR_HOMDEL = "#0000ff"
+
+MUT_COLOR_FUSION = "#C900A1"
+STRUCTURAL_VARIANT_COLOR = "#8B00C9"
+STRUCTURAL_VARIANT_PASSENGER_COLOR = "#ce92e8"
+
+DEFAULT_GREY = "#BEBEBE"
+
+
+class Alteration(Enum):
+    BACKGROUND = auto()
+    AMP = auto()
+    GAIN = auto()
+    HOMDEL = auto()
+    HETLOSS = auto()
+    MRNA_HIGH = auto()
+    MRNA_LOW = auto()
+    PROTEIN_HIGH = auto()
+    PROTEIN_LOW = auto()
+    FUSION = auto()
+    GERMLINE = auto()
+    SPLICE = auto()
+    SPLICE_PASSENGER = auto()
+    MISSENSE = auto()
+    MISSENSE_PASSENGER = auto()
+    PROMOTER = auto()
+    TRUNC = auto()
+    TRUNC_PASSENGER = auto()
+    INFRAME = auto()
+    INFRAME_PASSENGER = auto()
+    STRUCTURAL_VARIANT = auto()
+    STRUCTURAL_VARIANT_PASSENGER = auto()
+    # STRUCTURE_VARIANT
+
+    OTHER = 10000
+
+
+# Overwrite the default legend
+# So that the legend entry will add a background
+class _AltPiece:
+    background_color = None
+
+    def legend(self, x, y, w, h):
+        arts = []
+        if self.background_color is not None:
+            arts.append(Rectangle((x, y), w, h, facecolor=self.background_color))
+        arts.append(self.draw(x, y, w, h, None))
+        return PatchCollection(arts, match_original=True)
+
+
+class Rect(_AltPiece, mlayers.Rect):
+    pass
+
+
+class FrameRect(_AltPiece, mlayers.FrameRect):
+    pass
+
+
+class FracRect(_AltPiece, mlayers.FracRect):
+    pass
+
+
+@dataclass(repr=False)
+class MatchRule:
+    startswith: str = None
+    endswith: str = None
+    contains: List[str] = field(default_factory=list)
+    flexible: bool = False
+
+    def is_match(self, text: str):
+        text = text.lower()
+
+        match_start = not self.flexible
+        if self.startswith is not None:
+            match_start = text.startswith(self.startswith)
+
+        match_end = not self.flexible
+        if self.endswith is not None:
+            match_end = text.endswith(self.endswith)
+
+        match_contains = True
+        if len(self.contains) > 0:
+            match_contains = np.sum([i in text for i in self.contains])
+
+        if self.flexible:
+            return match_start | match_end | match_contains
+        else:
+            return match_start & match_end & match_contains
+
+
+MATCH_POOL = {
+    Alteration.AMP: MatchRule(startswith="amp"),
+    Alteration.GAIN: MatchRule(startswith="gain"),
+    Alteration.HOMDEL: MatchRule(
+        startswith="homdel", contains=["deep", "deletion"], flexible=True
+    ),
+    Alteration.HETLOSS: MatchRule(
+        startswith="hetloss", contains=["shallow", "deletion"], flexible=True
+    ),
+    Alteration.MRNA_HIGH: MatchRule(contains=["mrna", "high"]),
+    Alteration.MRNA_LOW: MatchRule(contains=["mrna", "low"]),
+    Alteration.PROTEIN_HIGH: MatchRule(contains=["protein", "high"]),
+    Alteration.PROTEIN_LOW: MatchRule(contains=["protein", "low"]),
+    Alteration.FUSION: MatchRule(startswith="fusion"),
+    Alteration.GERMLINE: MatchRule(startswith="germline"),
+    Alteration.MISSENSE_PASSENGER: MatchRule(
+        startswith="missense", contains=["passenger"]
+    ),
+    Alteration.MISSENSE: MatchRule(
+        startswith="missense", contains=["driver"], flexible=True
+    ),
+    Alteration.PROMOTER: MatchRule(startswith="promoter"),
+    Alteration.TRUNC_PASSENGER: MatchRule(startswith="trunc", contains=["passenger"]),
+    Alteration.TRUNC: MatchRule(startswith="trunc"),
+    Alteration.INFRAME_PASSENGER: MatchRule(
+        startswith="inframe", contains=["passenger"]
+    ),
+    Alteration.INFRAME: MatchRule(startswith="inframe"),
+    Alteration.STRUCTURAL_VARIANT_PASSENGER: MatchRule(
+        startswith="sv", contains=["structural", "variant", "passenger"], flexible=True
+    ),
+    Alteration.STRUCTURAL_VARIANT: MatchRule(
+        startswith="sv", contains=["structural", "variant"], flexible=True
+    ),
+    Alteration.SPLICE_PASSENGER: MatchRule(startswith="splice", contains=["passenger"]),
+    Alteration.SPLICE: MatchRule(startswith="splice"),
+}
+
+SHAPE_BANK = {
+    Alteration.BACKGROUND: Rect(
+        color=DEFAULT_GREY, label="No alterations", zorder=-10000
+    ),
+    # CNA
+    Alteration.AMP: Rect(color=CNA_COLOR_AMP, label="Amplification"),
+    # ShapeId.ampRectangle
+    Alteration.GAIN: Rect(color=CNA_COLOR_GAIN, label="Gain"),
+    # ShapeId.gainRectangle
+    Alteration.HOMDEL: Rect(color=CNA_COLOR_HOMDEL, label="Deep Deletion"),
+    Alteration.HETLOSS: Rect(color=CNA_COLOR_HETLOSS, label="Shallow Deletion"),
+    # mRNA Regulation
+    Alteration.MRNA_HIGH: FrameRect(
+        color=MRNA_COLOR_HIGH, width=1.5, label="mRNA High", zorder=1000
+    ),
+    Alteration.MRNA_LOW: FrameRect(
+        color=MRNA_COLOR_LOW, width=1.5, label="mRNA Low", zorder=1000
+    ),
+    # Protein Expression Regulation
+    Alteration.PROTEIN_HIGH: FracRect(
+        color=PROT_COLOR_HIGH, frac=(1.0, 0.2), label="Protein High", zorder=100
+    ),
+    Alteration.PROTEIN_LOW: FracRect(
+        color=PROT_COLOR_LOW, frac=(1.0, 0.2), label="Protein Low", zorder=100
+    ),
+    # Structural variant
+    Alteration.STRUCTURAL_VARIANT: FracRect(
+        color=STRUCTURAL_VARIANT_COLOR,
+        frac=(1.0, 0.6),
+        label="Structural variant",
+        zorder=200,
+    ),
+    Alteration.STRUCTURAL_VARIANT_PASSENGER: FracRect(
+        color=STRUCTURAL_VARIANT_PASSENGER_COLOR,
+        frac=(1.0, 0.6),
+        label="Structural variant (putative passenger)",
+        zorder=200,
+    ),
+    Alteration.FUSION: FracRect(
+        color=MUT_COLOR_FUSION, frac=(1.0, 0.6), label="Fusion", zorder=200
+    ),
+    # Splice
+    Alteration.SPLICE: FracRect(
+        color=MUT_COLOR_SPLICE, frac=(1.0, 0.3), label="Splice Mutation", zorder=400
+    ),
+    Alteration.SPLICE_PASSENGER: FracRect(
+        color=MUT_COLOR_SPLICE_PASSENGER,
+        frac=(1.0, 0.3),
+        label="Splice Mutation (putative passenger)",
+        zorder=400,
+    ),
+    Alteration.MISSENSE: FracRect(
+        color=MUT_COLOR_MISSENSE,
+        frac=(1.0, 0.3),
+        label="Mutation (putative driver)",
+        zorder=400,
+    ),
+    Alteration.MISSENSE_PASSENGER: FracRect(
+        color=MUT_COLOR_MISSENSE_PASSENGER,
+        frac=(1.0, 0.3),
+        label="Missense Mutation (putative passenger)",
+        zorder=400,
+    ),
+    Alteration.OTHER: FracRect(
+        color=MUT_COLOR_OTHER, frac=(1.0, 0.3), label="Other Mutation", zorder=400
+    ),
+    Alteration.PROMOTER: FracRect(
+        color=MUT_COLOR_PROMOTER, frac=(1.0, 0.3), label="Promoter Mutation", zorder=400
+    ),
+    Alteration.TRUNC: FracRect(
+        color=MUT_COLOR_TRUNC, frac=(1.0, 0.3), label="Truncating Mutation", zorder=400
+    ),
+    Alteration.TRUNC_PASSENGER: FracRect(
+        color=MUT_COLOR_TRUNC_PASSENGER,
+        frac=(1.0, 0.3),
+        label="Truncating Mutation (putative passenger)",
+        zorder=400,
+    ),
+    Alteration.INFRAME: FracRect(
+        color=MUT_COLOR_INFRAME,
+        frac=(1.0, 0.3),
+        label="Inframe Mutation (putative driver)",
+        zorder=400,
+    ),
+    Alteration.INFRAME_PASSENGER: FracRect(
+        color=MUT_COLOR_INFRAME_PASSENGER,
+        frac=(1.0, 0.3),
+        label="Inframe Mutation (putative passenger)",
+        zorder=400,
+    ),
+    # Germline
+    Alteration.GERMLINE: FracRect(
+        color=MUT_COLOR_GERMLINE, frac=(1.0, 0.1), label="Germline Mutation", zorder=600
+    ),
+}

marsilea-0.4.2.dist-info/METADATA

@@ -1,76 +0,0 @@
-Metadata-Version: 2.1
-Name: marsilea
-Version: 0.4.2
-Summary: Declarative creation of composable visualization
-Author: Zhihang Zheng
-Author-email: Mr-Milk <yzheng@cemm.at>
-Requires-Python: >=3.8
-Description-Content-Type: text/markdown
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python :: 3
-Classifier: Framework :: Matplotlib
-Requires-Dist: numpy
-Requires-Dist: pandas
-Requires-Dist: matplotlib>=3.6
-Requires-Dist: seaborn
-Requires-Dist: scipy
-Requires-Dist: legendkit
-Requires-Dist: platformdirs
-Requires-Dist: ruff ; extra == "dev"
-Requires-Dist: icecream ; extra == "dev"
-Requires-Dist: python-hmr ; extra == "dev"
-Requires-Dist: pytest ; extra == "dev"
-Requires-Dist: scikit-learn ; extra == "dev"
-Requires-Dist: sphinx ; extra == "dev"
-Requires-Dist: numpydoc ; extra == "dev"
-Requires-Dist: sphinx_design ; extra == "dev"
-Requires-Dist: pydata-sphinx-theme ; extra == "dev"
-Requires-Dist: sphinx-copybutton ; extra == "dev"
-Requires-Dist: sphinx_gallery ; extra == "dev"
-Requires-Dist: mpl_fontkit ; extra == "dev"
-Project-URL: Home, https://github.com/Marsilea-viz/marsilea
-Provides-Extra: dev
-
-<p align="center">
-  <picture align="center">
-    <source media="(prefers-color-scheme: dark)" srcset="https://github.com/Marsilea-viz/marsilea/raw/main/img/banner-dark.jpg">
-    <source media="(prefers-color-scheme: light)" srcset="https://github.com/Marsilea-viz/marsilea/raw/main/img/banner-blue.jpg">
-    <img alt="Shows a bar chart with benchmark results." src="https://github.com/Marsilea-viz/marsilea/raw/main/img/banner-dark.jpg" width="400">
-  </picture>
-</p>
-
-[![Documentation Status](https://img.shields.io/readthedocs/marsilea?color=57B77E&logo=readthedocs&logoColor=white&style=flat-square)](https://marsilea.readthedocs.io/en/stable)
-![pypi version](https://img.shields.io/pypi/v/marsilea?color=0098FF&logo=python&logoColor=white&style=flat-square)
-
-❗We are in beta, API may change and bugs expected
-
-### Declarative creation of composable visualization!
-
-[Read Documentation](https://marsilea.readthedocs.io/)
-
-
-### Installation
-
-```shell
-pip install marsilea
-```
-
-[//]: # (### Examples)
-
-[//]: # ()
-[//]: # (|                                                                                                                 |                                                                                                               |)
-
-[//]: # (|-----------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------|)
-
-[//]: # (|                                                     Heatmap                                                     |                                                   Oncoprint                                                   |)
-
-[//]: # (| <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_pbmc3k_001_2_00x.png" width=400>      | <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_oncoprint_005_2_00x.png" width=400> |)
-
-[//]: # (|                                                    Upsetplot                                                    |                                            Composition Stacked Bar                                            |)
-
-[//]: # (| <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_upset_001_2_00x.png" width=400>       | <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_oil_well_001_2_00x.png" width=400>  |)
-
-[//]: # (|                                                   Arc Diagram                                                   |                                           Protein sequence alignment                                          |)
-
-[//]: # (| <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_arc_diagram_001_2_00x.png" width=400> | <img src="https://marsilea.readthedocs.io/en/latest/_images/sphx_glr_plot_seqalign_001_2_00x.png" width=400>  |)
-