✨ Add density_scatter plotting function

pyproject.toml

@@ -17,7 +17,8 @@ dependencies = [
     "scipy",
     "seaborn",
     "matplotlib",
-    "readfcs"
+    "readfcs",
+    "datashader"
 ]
 
 [project.urls]

pytometry/plotting/_scatter_density.py

@@ -0,0 +1,94 @@
+import datashader as ds
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+import scanpy as sc
+from anndata import AnnData
+from datashader.mpl_ext import dsshow
+
+
+def scatter_density(
+    adata: AnnData,
+    x="FSC-A",
+    y="SSC-A",
+    x_label="FSC-A",
+    y_label="SSC-A",
+    x_scale="linear",
+    y_scale="linear",
+    x_lim=[-2 * 1e4, 3 * 1e5],
+    y_lim=[-2 * 1e4, 3 * 1e5],
+    ax=None,
+    cmap="jet",
+    vmin=None,
+    vmax=None,
+):
+    """Plots the cell density across two adata.obs.
+
+    Args:
+        adata (AnnData): AnnData object containing data.
+        x (str): adata.obs to plot on x axis.
+            Defaults to 'FSC-A'
+        y (str): adata.obs to plot on x axis.
+            Defaults to 'SSC-A'.
+        x_label (str): x axis label.
+        y_label (str): y axis label.
+        x_scale (str{"linear", "log", "symlog", "logit", ...}):
+            x axis scale type to apply.
+            Defaults to 'linear'.
+        y_scale (str{"linear", "log", "symlog", "logit", ...}):
+            y axis scale type to apply.
+            Defaults to 'linear'.
+        x_lim (list): upper and lower limit of the x axis.
+        y_lim (list): upper and lower limit of the y axis.
+        ax (`matplotlib.Axes`), optional:
+            Axes to draw into. If *None*, create a new figure or use ``fignum`` to
+            draw into an existing figure.
+        cmap (str or list or :class:`matplotlib.cm.Colormap`), optional:
+            For scalar aggregates, a matplotlib colormap name or instance.
+            Alternatively, an iterable of colors can be passed and will be converted
+            to a colormap. For a single-color, transparency-based colormap, see
+            :func:`alpha_colormap`.
+            Defaults to 'jet'.
+        vmin, vmax (float), optional:
+            For scalar aggregates, the data range that the colormap covers.
+            If vmin or vmax is None (default), the colormap autoscales to the
+            range of data in the area displayed, unless the corresponding value is
+            already set in the norm.
+
+    Returns:
+        Scatter plot that displays cell density
+    """
+    fig, ax = plt.subplots()
+    # Create df from anndata object
+    markers = [x, y]
+    joined = sc.get.obs_df(adata, keys=[*markers])
+
+    # Convert variables to np.array
+    x = np.array(joined[x])
+    y = np.array(joined[y])
+
+    # Plot density with datashader
+    df = pd.DataFrame(dict(x=x, y=y))
+    dsartist = dsshow(
+        df,
+        ds.Point("x", "y"),
+        ds.count(),
+        vmin=vmin,
+        vmax=vmax,
+        norm=None,
+        # aspect="auto",
+        ax=ax,
+        cmap=cmap,
+    )
+
+    plt.colorbar(dsartist)
+
+    plt.xlim(x_lim)
+    plt.ylim(y_lim)
+    plt.yscale(x_scale)
+    plt.xscale(y_scale)
+    plt.xlabel(x_label)
+    plt.ylabel(y_label)
+
+    plt.show()
+    return