dotools_py.pl.density

dotools_py.pl.density(adata, color, figsize=(6, 5), ax=None, ncols=4, cmap='Reds', palette=None, show=True, vmax=None, vmin=None, vcenter=None, color_legend_title=None, density_legend_title=None, path=None, filename='Density.pdf', basis='spatial', show_basis=True, density_alpha=0.75, density_bw_adjust=0.5, fill=True, gridsize=200, kwargs_kde=None, **kwargs)

Density plot.

Parameters:

adata AnnData

Annotated data matrix.

color str | list

Value in adata.var_names or column name in adata.obs

figsize tuple[float, float] (default: (6, 5))

Figure size, the format is (width, height)

ax Axes (default: None)

Matplotlib axes.

ncols int (default: 4)

Number of columns per row when multiple values are plotted.

cmap str (default: 'Reds')

String denoting matplotlib color map.

palette dict (default: None)

Colors to use for plotting categorical annotation groups in dictionary format with group as key and color as the value. If None, categorical variable with already colors stored in adata.uns[“{var}_colors”] will be used.

show bool (default: True)

If set to False, returns a dictionary with the matplotlib axes.

vmax int | str (default: None)

The value representing the upper limit of the color scale.

vmin int | str (default: None)

The value representing the lower limit of the color scale.

vcenter int | str (default: None)

The value representing the center of the color scale.

color_legend_title str (default: None)

Title of the colorbar legend

density_legend_title str (default: None)

Title of the colorbar for the density

path str | PathLike[str] | Path (default: None)

Folder where the figure is saved.

filename str (default: 'Density.pdf')

Name of the file.

basis str (default: 'spatial')

Embedding to use, default spatial.

show_basis bool (default: True)

If set to True both the density and the scatterplot for the embedding will be shown.

density_alpha float (default: 0.75)

Transparency for the density kernel.

density_bw_adjust float (default: 0.5)

Factor that multiplicatively scales the value chosen using bw_method. Increasing will make the curve smoother.

fill bool (default: True)

If True, fill in the area under univariate density curves or between bivariate contours.

gridsize int (default: 200)

Number of points on each dimension of the evaluation grid. A smaller number mights speed up plot generation.

kwargs_kde dict (default: None)

Additional arguments pass to sns.kdeplot

kwargs

Additional arguments pass to dotools_py.pl.embedding.

Return type:

Axes | None

Returns:

Depending on show, returns the plot if set to True or a dictionary with the axes.

Examples

Visualize a categorical column

import dotools_py as do
adata = do.dt.example_10x_processed()
do.pl.density(adata, 'annotation', basis="X_umap", density_alpha=1, show_basis=False)

or the expression of a gene

do.pl.density(adata, 'CD4', basis="X_umap", density_alpha=.75)