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.
- 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_scaleint 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}_clusterbool or None
If True, cluster the {rows, columns}.
- contextNone, or one of {paper, notebook, talk, poster}
A dictionary of parameters or the name of a preconfigured set.
- font_scalefloat, 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.
- Returns
If show==False a matplotlib.Axis
- adata: