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

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/plotter/_images.py

@@ -1,99 +0,0 @@
-# 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
-
-import numpy as np
-from matplotlib.image import imread, BboxImage
-from matplotlib.transforms import Bbox
-from pathlib import Path
-from platformdirs import user_cache_dir
-from urllib.request import urlretrieve
-
-from .base import RenderPlan
-
-TWEMOJI_CDN = "https://cdn.jsdelivr.net/gh/twitter/twemoji/assets/72x72/"
-
-
-def _cache_remote(url, cache=True):
-    data_dir = Path(user_cache_dir(appname="Marsilea"))
-    data_dir.mkdir(exist_ok=True, parents=True)
-
-    fname = url.split("/")[-1]
-    dest = data_dir / fname
-    if not (cache and dest.exists()):
-        urlretrieve(url, dest)
-
-    return dest
-
-
-class Emoji(RenderPlan):
-    def __init__(self, images, lang="en", scale=1, mode="filled"):
-        try:
-            import emoji
-        except ImportError:
-            raise ImportError("Required emoji, try `pip install emoji`.")
-
-        codes = []
-        for i in images:
-            i = emoji.emojize(i, language=lang)
-            if not emoji.is_emoji(i):
-                raise ValueError(f"{i} is not a valid emoji")
-            codes.append(f"{ord(i):X}".lower())
-
-        self.set_data(np.asarray(codes))
-        self.emoji_caches = {}
-        for c in codes:
-            cache_image = _cache_remote(f"{TWEMOJI_CDN}{c}.png")
-            self.emoji_caches[c] = imread(cache_image)
-
-        self.scale = scale
-        self.mode = mode
-
-    def _get_images_bbox(self, figure, imgs):
-        for img in imgs:
-            width, height = img.shape[:2]
-
-        return Bbox.from_bounds(0, 0, width, height)
-
-    def render_ax(self, spec):
-        ax = spec.ax
-        data = spec.data
-
-        # TODO: Does not work for orient = "v"
-        locs = np.linspace(0, 1, len(data) + 1)
-        for loc, d in zip(locs, data):
-            img = self.emoji_caches[d]
-            width, height = img.shape[:2]
-
-            xmin, ymin = ax.transAxes.transform((0, 0))
-            xmax, ymax = ax.transAxes.transform((1, 1))
-
-            ax_width = xmax - xmin
-            ax_height = ymax - ymin
-
-            fit_width = ax_width / len(data)
-            fit_height = height / width * fit_width
-
-            fit_scale_width = fit_width * self.scale
-            fit_scale_height = fit_height * self.scale
-
-            offset = (fit_width - fit_scale_width) / 2 / ax_width
-            loc += offset
-
-            loc_y = 0.5 - fit_scale_height / 2 / ax_height
-
-            def get_emoji_bbox(renderer, loc, loc_y, width, height):
-                x0, y0 = ax.transData.transform((loc, loc_y))
-                return Bbox.from_bounds(x0, y0, width, height)
-
-            partial_get_emoji_bbox = partial(
-                get_emoji_bbox,
-                loc=loc,
-                loc_y=loc_y,
-                width=fit_scale_width,
-                height=fit_scale_height,
-            )
-
-            i1 = BboxImage(partial_get_emoji_bbox, data=img)
-            ax.add_artist(i1)

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>  |)
-

marsilea-0.4.2.dist-info/RECORD

@@ -1,27 +0,0 @@
-marsilea/__init__.py,sha256=d0Ly-YfvxU50ILe2FqnmpvcnSg6XwCHVIh1LRIqQfNE,541
-marsilea/_api.py,sha256=tymWZHfjhx8-0NNd9762znfdIu36NrARRweEIr5L1mA,283
-marsilea/_deform.py,sha256=SKXLvhyUrwTRAw7Fl--OpupDLk6T3S5DRfwCAdewHQs,14138
-marsilea/base.py,sha256=HSY25Ax39Vj80FxSZkg4es0YklNtFJ_DgfQzbFIJseI,46637
-marsilea/dataset.py,sha256=a0mXjPu9_tRGHofnnQaTryFpxftkfqldq_ZLXMSBf7A,4410
-marsilea/dendrogram.py,sha256=WUnV2JMSY9mPt1sfkFAEikkl2ta7xHFD13teas_iZgE,14767
-marsilea/exceptions.py,sha256=kIXDRF8Fy-BkNqeMbLqde06PaWESuKiGCMGyDpVpWIE,1006
-marsilea/heatmap.py,sha256=lKGt0lTtziNFDsb_SBfFt3zoYzVYRzezc9aae5RxHyk,4168
-marsilea/layers.py,sha256=puXLlGGpEqAzaTqadpgpsYmIDPH33WyyHIuysRSqFZQ,12163
-marsilea/layout.py,sha256=X8MGPlAbbr7dcZiqW4pI7sEb8U3jVaiS7t1DKOqMYLI,27758
-marsilea/upset.py,sha256=U1Rsmo1WpCAV9z3LBlE2L4T0nAW9ols8Z36fXzmXycw,30388
-marsilea/utils.py,sha256=LJ7U0aVw_Ru45DXo4x5zi1FEjjIKt4j0mpdDY34wiNA,2903
-marsilea/plotter/__init__.py,sha256=n1E53C5oqnsHZcXAtN6HgZsZdcAvANONNx-fupTxzN0,738
-marsilea/plotter/_images.py,sha256=RWCI4FhcxJZimLrhdy9CHw3ri1kweGRICUyByE4wzmg,3065
-marsilea/plotter/_seaborn.py,sha256=aK0EnboshfNCNvNjsIc7dxDE_4KBKi4HMUt7CKWt_6U,8188
-marsilea/plotter/_utils.py,sha256=Efhdk-TrrAanhbXRiEVWThMYvZ4vVHZMVYMs5X3JvIM,710
-marsilea/plotter/arc.py,sha256=PFXlJ0TBIJ1mEB-lIl-Zs2UdEXkLSwDlRJbsSa5Ss5U,8165
-marsilea/plotter/area.py,sha256=zjjAhvgKHYe9rqzcseqZqhwfpgvzm0w2FRJ_vr9Fxm4,2650
-marsilea/plotter/bar.py,sha256=TeX6li--kE9NtqCRflDTX0jkG1-uIq0Dn8ILKSv-AuA,12080
-marsilea/plotter/base.py,sha256=NgaoFnbMS6Mj4BghVcGaSYYN8A9e3DD_rRomDIm4C5c,20456
-marsilea/plotter/bio.py,sha256=_pZkGoAei7eirFCpu7AcZJhebBneNjUKcZlI36bpqUE,5044
-marsilea/plotter/mesh.py,sha256=YY6aq62QS1HyTeIWF79rpIJUUQTOxWXx3LZ7oZXYlzU,23797
-marsilea/plotter/text.py,sha256=oYJ5py3_nGHKi60DSVzFgPg4drnTSTw__IcYs0cut4M,36222
-marsilea-0.4.2.dist-info/LICENSE,sha256=2TLD8FnLJqXzg8YBRs7W3VZBwfWfp4ArDfBl-rn96Qc,1074
-marsilea-0.4.2.dist-info/WHEEL,sha256=EZbGkh7Ie4PoZfRQ8I0ZuP9VklN_TvcZ6DSE5Uar4z4,81
-marsilea-0.4.2.dist-info/METADATA,sha256=3H95A_-TertDPICUSKoJECa8Hf29atnkEYs28p00lLE,4074
-marsilea-0.4.2.dist-info/RECORD,,