pytometry.pl.scatter_density

pytometry.pl.scatter_density#

pytometry.pl.scatter_density(adata, x='FSC-A', y='SSC-A', x_label=None, y_label=None, x_scale='linear', y_scale='linear', x_lim=None, y_lim=None, ax=None, figsize=None, bins=500, cmap='jet', vmin=None, vmax=None, *, layer=None)#

Plots the cell density across two adata.obs.

Parameters:

  • adata (AnnData) – AnnData object containing data.

  • x (str (default: 'FSC-A')) – adata.obs to plot on x axis.

  • y (str (default: 'SSC-A')) – adata.obs to plot on x axis.

  • x_label (str | None (default: None)) – x axis label.

  • y_label (str | None (default: None)) – y axis label.

  • x_scale (Union[ScaleBase, Literal['linear', 'log', 'symlog', 'logit']] (default: 'linear')) – x axis scale type to apply.

  • y_scale (Union[ScaleBase, Literal['linear', 'log', 'symlog', 'logit']] (default: 'linear')) – y axis scale type to apply.

  • x_lim (tuple[float, float] | None (default: None)) – upper and lower limit of the x axis.

  • y_lim (tuple[float, float] | None (default: None)) – upper and lower limit of the y axis.

  • ax (Axes | None (default: None)) – Axes to draw into. If None, create a new figure or use fignum to draw into an existing figure.

  • figsize (tuple[int, int] | None (default: None)) – Figure size (width, height) if ax not provided.

  • bins (int | tuple[int, int] (default: 500)) – Number of bins for the np.histogram2d function.

  • cmap (str | Colormap (default: 'jet')) – For scalar aggregates, a matplotlib colormap name or instance. Alternatively, an iterable of colors can be passed and will be converted to a colormap.

  • vmin (float | None (default: None)) – 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.

  • vmax (float | None (default: None)) – 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.

  • layer (str | None (default: None)) – The layer in adata to use. If None, use adata.X.

Return type:

None

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