Basic scatter plot

src/anndata_plot/pl/__init__.py

@@ -1 +1,16 @@
 from .basic import BasicClass, basic_plot
+
+from .scatter import scatter
+
+from .render_utils import ColorOpts
+from .render_utils import LegendOpts
+from .render_utils import SizeOpts
+from .render_utils import AxisOpts
+
+__all__ = [
+    "scatter",
+    "ColorOpts",
+    "LegendOpts",
+    "SizeOpts",
+    "AxisOpts",
+]

src/anndata_plot/pl/_utils.py

@@ -0,0 +1,24 @@
+from typing import Literal
+
+_FontWeight = Literal["light", "normal", "medium", "semibold", "bold", "heavy", "black"]
+_FontSize = Literal[
+    "xx-small", "x-small", "small", "medium", "large", "x-large", "xx-large"
+]
+_LegendLoc = Literal[
+    "none",
+    "right margin",
+    "on data",
+    "on data export",
+    "best",
+    "upper right",
+    "upper left",
+    "lower left",
+    "lower right",
+    "right",
+    "center left",
+    "center right",
+    "lower center",
+    "upper center",
+    "center",
+]
+ColorLike = str | tuple[float, ...]

src/anndata_plot/pl/render_utils.py

@@ -0,0 +1,52 @@
+from dataclasses import dataclass
+
+from typing import Literal
+
+_LegendLoc = Literal[
+    "none",
+    "right margin",
+    "on data",
+    "on data export",
+    "best",
+    "upper right",
+    "upper left",
+    "lower left",
+    "lower right",
+    "right",
+    "center left",
+    "center right",
+    "lower center",
+    "upper center",
+    "center",
+]
+_FontWeight = Literal["light", "normal", "medium", "semibold", "bold", "heavy", "black"]
+_FontSize = Literal[
+    "xx-small", "x-small", "small", "medium", "large", "x-large", "xx-large"
+]
+
+@dataclass
+class LegendOpts:
+    legend_position: str = "inner"
+    legend_cols: int = 1
+    show_legend: bool = True
+
+@dataclass
+class LegendOptsMpl(LegendOpts):
+    legend_font_weight: _FontWeight = "normal"
+    legend_font_size: _FontSize = "medium"
+
+
+
+@dataclass
+class ColorOpts:
+    color: str = "blue"
+    cmap: str = "viridis"
+
+@dataclass
+class SizeOpts:
+    size: int = 100
+
+@dataclass
+class AxisOpts:
+    xlabel: str = ""
+    ylabel: str = ""

src/anndata_plot/pl/scatter.py

@@ -0,0 +1,138 @@
+from ._utils import ColorLike
+from typing import Literal, Sequence
+import numpy as np
+import pandas as pd
+
+from typing import Collection
+from numpy.typing import NDArray
+
+from .render_utils import ColorOpts
+from .render_utils import LegendOpts
+from .render_utils import SizeOpts
+from .render_utils import AxisOpts
+from .render_utils import _LegendLoc
+from .render_utils import _FontWeight
+from .render_utils import _FontSize
+
+from dataclasses import asdict
+
+from matplotlib.colors import is_color_like
+
+from anndata import AnnData
+
+import holoviews as hv
+
+# copied from scanpy, pl._anndata line +- 235
+# adapted to work with 1 color, that can only be in names or be a column
+def _check_if_annotations(
+    adata: AnnData,
+    axis_name: Literal["obs", "var"],
+    x: str | None = None,
+    y: str | None = None,
+    color: Collection[str | ColorLike] | None = None,
+    use_raw: bool | None = None,
+) -> bool:
+    """Check if `x`, `y`, and `colors` are annotations of `adata`.
+
+    If `axis_name` is `obs`, checks in `adata.obs.columns` and `adata.var_names`,
+    if `axis_name` is `var`, checks in `adata.var.columns` and `adata.obs_names`.
+    """
+    annotations: pd.Index[str] = getattr(adata, axis_name).columns
+    other_ax_obj = (
+        adata.raw if use_raw and axis_name == "obs" else adata
+    )
+    names: pd.Index[str] = getattr(
+        other_ax_obj, "var" if axis_name == "obs" else "obs"
+    ).index
+
+    def is_annotation(needle: pd.Index) -> NDArray[np.bool_]:
+        return needle.isin({None}) | needle.isin(annotations) | needle.isin(names)
+
+    if not is_annotation(pd.Index([x, y])).all():
+        return False
+
+    return bool(is_annotation(pd.Index([color])).all())
+
+def scatter(
+    adata: AnnData,
+    x: str | None = None,
+    y: str | None = None,
+    basis: str | None = None,
+    color_by: str | None = None,
+    title: str | None = None,
+    color_opts: ColorOpts | dict | None = None,
+    legend_opts: LegendOpts | dict | None = None,
+    size_opts: SizeOpts | dict | None = None,
+    interactive: bool = False,
+):
+
+    # determine which dims to use
+    if basis is not None:
+        kdims = [f"obsm.X_{basis}.0", f"obsm.X_{basis}.1"]
+        vdims = []
+        if color_by is not None and color_by in adata.obs.columns:
+            vdims = [f"obs.{color_by}"] if color_by is not None else []
+        elif color_by is not None and color_by in adata.var_names:
+            vdims = [color_by]
+    elif _check_if_annotations(adata, "obs", x=x, y=y, color = color_by):
+        kdims = [f"obs.{x}", f"obs.{y}"]
+        vdims = [f"obs.{color_by}"] if color_by is not None else []
+    elif _check_if_annotations(adata, "var", x=x, y=y, color = color_by):
+        kdims = [f"var.{x}", f"var.{y}"]
+        vdims = [f"var.{color_by}"] if color_by is not None else []
+    else:
+        msg = (
+            "`x`, `y`, and potential `color` inputs must all "
+            "come from either `.obs` or `.var`"
+        )
+        raise ValueError(msg)
+
+    if title is None and color_by is not None:
+        title = color_by.replace("_", " ")
+
+    title_opts = {"title": title}
+
+    if interactive:
+        allopts = get_interactive_opts(vdims[0])
+    else:
+        allopts = get_static_opts(vdims[0])
+
+    all_opts = {
+        **title_opts,
+        **allopts
+    }
+
+    return hv.Points(adata, kdims, vdims).opts(**all_opts)
+
+def get_color_opts(kdims, vdims, interactive, color_by = None, cmap = None, palette = None, **kwargs):
+    args = {}
+
+    if len(vdims) != 0:
+        args["color"] = vdims[0]
+    if palette is not None:
+        args["cmap"] = palette
+    if cmap is not None:
+        args["cmap"] = cmap
+    return ColorOpts(**args)
+
+def get_legend_opts(legend_loc = None, interactive = False, **kwargs):
+    if legend_loc is not None:
+        return LegendOpts(legend_position = legend_loc, **kwargs)
+    return LegendOpts(**kwargs)
+
+
+def get_interactive_opts(color_by):
+    return {
+        "cmap": "viridis",
+        "color": color_by,
+        "width": 550,
+        "height": 550,
+        "legend_position": "bottom_left"
+    }
+
+def get_static_opts(color_by):
+    return {
+        "cmap": "viridis",
+        "color": color_by,
+        "fig_size": 250,
+    }