ocelli.pl.scatter

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ocelli.pl.scatter#

ocelli.pl.scatter(adata: AnnData, x: str, s: float = 1.0, c: str | None = None, cdict: dict | None = None, cmap=None, vmin=None, vmax=None, xlim: tuple | None = None, ylim: tuple | None = None, figsize=None, ncols: int = 4, fontsize: int = 6, title: str | None = None, showlegend: bool = True, markerscale: float = 1.0, save: str | None = None, dpi: int = 300)#

2D scatter plots

This function creates a 2D scatter plot based on data stored in adata.obsm and optionally colors the points using a single (adata.obs) or multiple (adata.obsm) color schemes. For multiple color schemes, a grid of plots is generated.

Parameters:

  • adata (anndata.AnnData) – The annotated data matrix.

  • x (str) – Key in adata.obsm containing the 2D data for plotting.

  • s (float) – Size of the scatter plot markers. (default: 1.0)

  • c (str or None) – Key in adata.obs or adata.obsm specifying the color scheme. (default: None)

  • cdict (dict or None) – A dictionary mapping discrete groups in the color scheme to specific colors. Used for discrete color schemes. (default: None)

  • cmap (str or None) – Colormap for continuous color schemes. Can be a string name of a Matplotlib colormap or a custom colormap. (default: None)

  • vmin (float or None) – Lower bound of the colormap for continuous color schemes. (default: None)

  • vmax (float or None) – Upper bound of the colormap for continuous color schemes. (default: None)

  • xlim (tuple or None) – Tuple defining the x-axis limits. (default: None)

  • ylim (tuple or None) – Tuple defining the y-axis limits. (default: None)

  • figsize (tuple or None) – Tuple specifying the figure size. (default: None)

  • ncols (int) – Number of columns in the grid when plotting multiple color schemes from adata.obsm. (default: 4)

  • fontsize (int) – Font size for plot labels and titles. (default: 6)

  • title (str or None) – Title of the plot. If multiple plots are generated, this applies to each subplot. (default: None)

  • showlegend (bool) – Whether to display a legend for discrete color schemes. (default: True)

  • markerscale (float) – Scale of the legend markers. (default: 1.0)

  • save (str or None) – Path to save the plot as a file. If None, the plot is returned as a Matplotlib figure. (default: None)

  • dpi (int) – Resolution of the saved figure in dots per inch (DPI). (default: 300)

Returns:

  • If save is None, returns a Matplotlib figure object.

  • Otherwise, saves the plot to the specified path and does not return anything.

Return type:

matplotlib.figure.Figure or None

Example:
import ocelli as oci
from anndata import AnnData
import numpy as np

# Example data
adata = AnnData(X=np.random.rand(100, 50))
adata.obsm["embedding"] = np.random.rand(100, 2)
adata.obs["group"] = np.random.choice(["A", "B", "C"], 100)

# Generate scatter plot
oci.pl.scatter(adata, x="embedding", c="group", s=5, title="Scatter Plot Example")
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