ehrapy.plot.paga_path¶
- ehrapy.plot.paga_path(adata, nodes, keys, use_raw=True, annotations=('dpt_pseudotime',), color_map=None, color_maps_annotations=mappingproxy({'dpt_pseudotime': 'Greys'}), palette_groups=None, n_avg=1, groups_key=None, xlim=(None, None), title=None, left_margin=None, ytick_fontsize=None, title_fontsize=None, show_node_names=True, show_yticks=True, show_colorbar=True, legend_fontsize=None, legend_fontweight=None, normalize_to_zero_one=False, as_heatmap=True, return_data=False, show=None, save=None, ax=None)[source]¶
Feature changes along paths in the abstracted graph.
- Parameters:
adata (
AnnData
) –AnnData
object object containing all observations.nodes (
Sequence
[str
|int
]) – A path through nodes of the abstracted graph, that is, names or indices (within .categories) of groups that have been used to run PAGA.keys (
Sequence
[str
]) – Either variables in adata.var_names or annotations in adata.obs. They are plotted using color_map.use_raw (
bool
) – Use adata.raw for retrieving feature values if it has been set.annotations (
Sequence
[str
]) – Plot these keys with color_maps_annotations. Need to be keys for adata.obs.color_maps_annotations (
Mapping
[str
,str
|Colormap
]) – Color maps for plotting the annotations. Keys of the dictionary must appear in annotations.palette_groups (
Sequence
[str
] |None
) – Usually, use the same sc.pl.palettes… as used for coloring the abstracted graph.n_avg (
int
) – Number of data points to include in computation of running average.groups_key (
str
|None
) – Key of the grouping used to run PAGA. If None, defaults to adata.uns[‘paga’][‘groups’].left_margin – Margin to the left of the plot.
show_node_names (
bool
) – Whether to plot the node names on the nodes bar.show_yticks (
bool
) – Whether to show the y axis ticks.show_colorbar (
bool
) – Whether to show the color bar.legend_fontsize (
Union
[int
,float
,Literal
['xx-small'
,'x-small'
,'small'
,'medium'
,'large'
,'x-large'
,'xx-large'
],None
]) – Font size of the legend.legend_fontweight (
Union
[int
,Literal
['light'
,'normal'
,'medium'
,'semibold'
,'bold'
,'heavy'
,'black'
],None
]) – Font weight of the legend.normalize_to_zero_one (
bool
) – Shift and scale the running average to [0, 1] per feature.as_heatmap (
bool
) – Whether to display the plot as heatmap.return_data (
bool
) – Whether to return the timeseries data in addition to the axes if True.save (
bool
|str
|None
) – Whether or where to save the plot.
- Return type:
- Returns:
A
Axes
object, if ax is None, else None. If return_data, return the timeseries data in addition to an axes.