ehrapy.plot.paga_compare#
- ehrapy.plot.paga_compare(adata, basis=None, edges=False, color=None, alpha=None, groups=None, components=None, projection='2d', legend_loc='on data', legend_fontsize=None, legend_fontweight='bold', legend_fontoutline=None, color_map=None, palette=None, frameon=False, size=None, title=None, right_margin=None, left_margin=0.05, show=None, save=None, title_graph=None, groups_graph=None, *, pos=None, **paga_graph_params)[source]#
Scatter and PAGA graph side-by-side.
Consists in a scatter plot and the abstracted graph. See
paga()
for all related parameters.- Parameters:
adata (
AnnData
) –AnnData
object object containing all observations.basis – String that denotes a plotting tool that computed coordinates.
edges – Whether to display edges.
color – Keys for annotations of observations/patients or features, or a hex color specification, e.g., ‘ann1’, ‘#fe57a1’, or [‘ann1’, ‘ann2’].
alpha – Alpha value for the image
groups – Key of the grouping used to run PAGA. If None, defaults to adata.uns[‘paga’][‘groups’].
components – For example,
'1,2,3'
means[1, 2, 3]
, first, second, third principal component.projection (
Literal
['2d'
,'3d'
]) – One of ‘2d’ or ‘3d’legend_loc – Location of the legend.
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'
]]) – Font weight of the legend.legend_fontoutline – Font outline of the legend.
color_map – Matplotlib color map.
palette – Matplotlib color palette.
frameon – Whether to display the labels frameon.
size – Size of the plot.
title – Title of the plot.
right_margin – Margin to the right of the plot.
left_margin – Margin to the left of the plot.
show – Whether to show the plot.
save – Whether or where to save the plot.
title_graph – The title of the graph.
groups_graph – Graph labels.
pos – Position of the plot.
**paga_graph_params – Keywords for
paga()
and keywords forscatter()
.
- Return type:
- Returns:
Matplotlib axes.