, var_names, sortby='latent_time', layer='Ms', color_map='viridis', col_color=None, palette='viridis', n_convolve=30, standard_scale=0, sort=True, colorbar=None, col_cluster=False, row_cluster=False, context=None, font_scale=None, figsize=(8, 4), show=None, save=None, **kwargs)

Plot time series for genes as heatmap.

adata : AnnData

Annotated data matrix.

var_names : str, list of str

Names of variables to use for the plot.

sortby : str (default: ‘latent_time’)

Observation key to extract time data from.

layer : str (default: ‘Ms’)

Layer key to extract count data from.

color_map : str (default: ‘viridis’)

String denoting matplotlib color map.

col_color : str or list of str (default: None)

String denoting matplotlib color map to use along the columns.

palette : list of str (default: ‘viridis’)

Colors to use for plotting groups (categorical annotation).

n_convolve : int or None (default: 30)

If int is given, data is smoothed by convolution along the x-axis with kernel size n_convolve.

standard_scale : int or None (default: 0)

Either 0 (rows) or 1 (columns). Whether or not to standardize that dimension (each row or column), subtract minimum and divide each by its maximum.

sort : bool (default: True)

Wether to sort the expression values given by xkey.

colorbar : bool or None (default: None)

Whether to show colorbar.

{row,col}_cluster : bool or None

If True, cluster the {rows, columns}.

context : None, or one of {paper, notebook, talk, poster}

A dictionary of parameters or the name of a preconfigured set.

font_scale : float, optional

Scaling factor to scale the size of the font elements.

figsize : tuple (default: (8,4))

Figure size.

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’}.


Arguments passed to seaborns clustermap, e.g., set yticklabels=True to display all gene names in all rows.


If show==False a matplotlib.Axis