pilotpy.pl.fit_pricipla_graph

pilotpy.pl.fit_pricipla_graph(adata, NumNodes=20, source_node=0, show_text=True, Do_PCA=False, figsize=(12, 12), X_color='r', Node_color='k', DimToPlot=[0, 1], facecolor='white', title='Principal graph')

Fit an Elastic Principal Graph to the data and extract pseudotime information.

Parameters

adataAnnData

Annotated data matrix containing embeddings and other necessary data.

NumNodesint, optional

Number of nodes for building the backbone, by default 20.

source_nodeint, optional

Index of the source node to start pseudotime estimation, by default 0.

show_textbool, optional

Whether to show numbers in the backbone plot, by default True.

Do_PCAbool, optional

Whether to perform PCA on the nodes, by default False.

figsizetuple, optional

Figsize, by default (12,12).

X_colorstr, optional

Color of the X-axis in the plot, by default ‘r’.

Node_colorstr, optional

Color of the backbone’s nodes, by default ‘k’.

DimToPlotlist, optional

List of integers specifying the PCs or dimensions to plot, by default [0, 1].

facecolorstr, optional

Background color of the figure, by default ‘white’.

titlestr, optional

Title of the plot, by default ‘Principal graph’.

Returns

None

Fits an Elastic Principal Graph, plots it, and extracts pseudotime information.