scanpy.pl.pca_overview

scanpy.pl.pca_overview(adata, **params)

Plot PCA results.

The parameters are the ones of the scatter plot. Call pca_ranking separately if you want to change the default settings.

Parameters

adata : AnnData

Annotated data matrix.

color : string or list of strings, optional (default: None)

Keys for observation/cell annotation either as list ["ann1", "ann2"] or string "ann1,ann2,...".

use_raw : bool, optional (default: True)

Use raw attribute of adata if present.

sort_order

For continuous annotations used as color parameter, plot data points with higher values on top of others.

groups

Restrict to a few categories in categorical observation annotation. The default is not to restrict to any groups.

components

For instance, ['1,2', '2,3']. To plot all available components use components='all'.

projection : {'2d', '3d'}, optional (default: '2d')

Projection of plot.

legend_loc

Location of legend, either ‘on data’, ‘right margin’ or valid keywords for matplotlib.legend.

legend_fontsize

Legend font size.

legend_fontweight : {‘normal’, ‘bold’, …}, optional (default: None)

Legend font weight. Defaults to ‘bold’ if legend_loc == 'on data', otherwise to ‘normal’. Available are ['light', 'normal', 'medium', 'semibold', 'bold', 'heavy', 'black'].

legend_fontoutline

Linewidth of the legend font outline. This uses matplotlib.patheffects to draw a white outline around the legend text.

size

Point size. If None, is automatically computed.

color_map

Color map to use for continous variables. Anything that works for cmap argument of pyplot.scatter should work here (e.g. "magma", "viridis", mpl.cm.cividis). If None value of mpl.rcParams["image.cmap"] is used.

palette

Colors to use for plotting categorical annotation groups. The palette can be a valid matplotlib.pyplot.colormap name like 'Set2' or 'tab20', a list of colors like ['red', '#ccdd11', (0.1, 0.2, 1)] or a Cycler object. If None, mpl.rcParams["axes.prop_cycle"] is used unless the categorical variable already has colors stored in adata.uns["{var}_colors"]. If provided, values of adata.uns["{var}_colors"] will be set by this palette.

frameon

Draw a frame around the scatter plot. Defaults to value set in set_figure_params(), defaults to True.

ncols

Number of panels per row.

wspace

Adjust the width of the space between multiple panels.

hspace

Adjust the height of the space between multiple panels.

title

Provide title for panels either as string or list of strings, e.g. ['title1', 'title2', ...].

kwargs : further keyword arguments, optional

Arguments to pass to matplotlib.pyplot.scatter(), for instance: the maximum and minimum values (e.g. vmin=-2, vmax=5).

return_fig

Return the matplotlib figure.

show : bool, optional (default: None)

Show the plot, do not return axis.

save : bool or str, optional (default: None)

If True or a str, save the figure. A string is appended to the default filename. Infer the filetype if ending on {‘.pdf’, ‘.png’, ‘.svg’}.