ocelli.pl.scatter_interactive

ocelli.pl.scatter_interactive#

ocelli.pl.scatter_interactive(adata: AnnData, x: str, s: float = 1.0, c: str | None = None, cdiscrete=None, ccontinuous=None, vmin=None, vmax=None, title=None, showlegend: bool = True, showaxes: bool = False, save=None)#

2D and 3D interactive scatter plots

Generates a 2D or 3D interactive scatter plot using Plotly. The plot is based on data stored in adata.obsm and can optionally use a color scheme from adata.obs.

Parameters:

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

  • x (str) – Key in adata.obsm containing 2D or 3D data for plotting.

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

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

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

  • ccontinuous (str or None) – Colormap for continuous color schemes. Options from Plotly’s colors.sequential, colors.diverging, or colors.cyclical. (default: None)

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

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

  • title (str or None) – Title of the plot. (default: None)

  • showlegend (bool) – Whether to display a legend. (default: True)

  • showaxes (bool) – Whether to display the plot axes. (default: False)

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

Returns:

  • If save=None: Returns a Plotly figure object.

  • Otherwise, saves the plot to the specified path as an HTML file.

Return type:

plotly.graph_objs._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 an interactive scatter plot
oci.pl.scatter_interactive(adata, x="embedding", c="group", s=5, title="Interactive Scatter Plot")