scvelo.pl.heatmap

scvelo.pl.heatmap(adata, 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.

Parameters:

  • 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 (bool or None) – If True, cluster the {rows, columns}.

  • 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’}.

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

Return type:

If show==False a matplotlib.Axis