"""Plate-layout plots."""
from __future__ import annotations
import re
from typing import TYPE_CHECKING, Any
import numpy as np
import pandas as pd
from mantispy._core._reduce import get_matrix, group_codes, group_offsets
from mantispy._core.frames import as_frame
from mantispy._core.plate import plate_grid, row_label, well_col, well_row
if TYPE_CHECKING:
from anndata import AnnData
from matplotlib.axes import Axes
#: How to combine rows falling in the same well; pandas skips NaN.
AGGREGATIONS = ("median", "mean", "max", "min")
def _values(adata: AnnData, color: str) -> np.ndarray:
"""The per-row quantity to draw, from either a feature or an ``obs`` column."""
if color in adata.var_names:
return get_matrix(adata)[:, adata.var_names.get_loc(color)].astype(float)
if color in adata.obs:
return as_frame(adata.obs)[color].to_numpy(dtype=float)
raise KeyError(f"{color!r} is neither a feature name nor an obs column")
def _natural(text: str) -> list[int | str]:
"""Sort key reading digit runs as numbers: source_2 before source_10."""
return [int(part) if part.isdigit() else part for part in re.split(r"(\d+)", text)]
[docs]
def plate(
adata: AnnData,
color: str,
plate: str | None = None,
groupby: str | None = None,
agg: str = "median",
ncols: int = 4,
share_colorbar: bool = True,
ax: Axes | None = None,
cmap: str = "viridis",
**kwargs: Any,
) -> Axes | np.ndarray:
"""Well-grid heatmap of ``color``, one panel per plate.
Args:
adata: Object to draw.
Works at cell or well resolution; several rows landing in the same well are combined with ``agg``.
color: A feature name or an ``obs`` column.
plate: Draw only this plate.
By default every plate gets a panel.
groupby: ``obs`` column, constant per plate, to order and title the panels by, such as ``"Metadata_Batch"``.
agg: How to combine rows sharing a well: median, mean, max or min.
ncols: Panels per row.
share_colorbar: One color scale and colorbar for all panels, instead of one per panel.
ax: Axes to draw into.
Only valid together with ``plate``.
cmap: Matplotlib colormap.
kwargs: Passed to :meth:`~matplotlib.axes.Axes.imshow`.
``vmin``, ``vmax`` or ``norm`` set the scale.
Returns:
A single :class:`~matplotlib.axes.Axes`, or an array of them for several plates in panel order, each panel labeled with the plate's own well grid.
Raises:
ValueError: ``agg`` is not one of ``AGGREGATIONS``, ``ax`` was passed for more than one plate, ``groupby`` varies within a drawn plate, or it or ``Metadata_Plate`` has missing values.
KeyError: ``color`` is neither a feature name nor an ``obs`` column, ``groupby`` is not an ``obs`` column, or ``plate`` is not a plate of ``adata``.
"""
import matplotlib.pyplot as plt
if agg not in AGGREGATIONS:
raise ValueError(f"agg must be one of {AGGREGATIONS}, got {agg!r}")
values = _values(adata, color)
codes, keys = group_codes(adata, [groupby, "Metadata_Plate"] if groupby else "Metadata_Plate")
panels = [key if isinstance(key, tuple) else (key,) for key in keys]
drawn = [index for index, panel in enumerate(panels) if plate is None or str(panel[-1]) == str(plate)]
if not drawn:
raise KeyError(f"obs has no plate {plate!r}")
if len({panels[index][-1] for index in drawn}) < len(drawn):
raise ValueError(f"{groupby!r} varies within a plate, so it cannot label one")
if ax is not None and len(drawn) > 1:
raise ValueError("pass plate= when supplying a single ax, or leave ax=None")
drawn.sort(key=lambda index: [_natural(str(part)) for part in panels[index]])
wells = pd.Categorical(as_frame(adata.obs)["Metadata_Well"])
positions = np.array([(well_row(well), well_col(well)) for well in wells.categories])[wells.codes]
order, offsets = group_offsets(codes, len(keys))
grids = []
for index in drawn:
rows = order[offsets[index] : offsets[index + 1]]
grid = np.full(plate_grid(wells.categories[np.unique(wells.codes[rows])]), np.nan)
combined = pd.Series(values[rows]).groupby([positions[rows, 0], positions[rows, 1]]).agg(agg)
grid[combined.index.get_level_values(0), combined.index.get_level_values(1)] = combined.to_numpy()
grids.append(grid)
if share_colorbar and "norm" not in kwargs:
everything = np.concatenate([grid.ravel() for grid in grids])
kwargs.setdefault("vmin", np.nanmin(everything))
kwargs.setdefault("vmax", np.nanmax(everything))
if ax is None:
width = min(ncols, len(grids))
height = -(-len(grids) // width)
figure = plt.figure(figsize=(4 * width, 3.2 * height))
axes = np.array([figure.add_subplot(height, width, number) for number in range(1, len(grids) + 1)])
else:
axes = np.array([ax])
for axis, grid, index in zip(axes, grids, drawn, strict=True):
image = axis.imshow(grid, cmap=cmap, aspect="equal", **kwargs)
axis.set_title(" · ".join(map(str, panels[index])), fontsize=9)
n_rows, n_cols = grid.shape
xticks, yticks = range(0, n_cols, max(1, n_cols // 12)), range(0, n_rows, max(1, n_rows // 16))
axis.set_xticks(xticks, [str(col + 1) for col in xticks], fontsize=7)
axis.set_yticks(yticks, [row_label(row) for row in yticks], fontsize=7)
if not share_colorbar:
axis.figure.colorbar(image, ax=axis, fraction=0.04, label=color)
if share_colorbar:
axes[0].figure.colorbar(image, ax=axes if len(axes) > 1 else axes[0], fraction=0.04, label=color)
return axes[0] if len(axes) == 1 else axes
