pilotpy.pl.trajectory
- pilotpy.pl.trajectory(adata, n_evecs=2, epsilon=1, alpha=0.5, knn=64, sample_col=1, clusters='status', label_act=False, colors=['#377eb8', '#ff7f00', '#e41a1c'], location_labels='center', figsize=(12, 12), font_size=24, axes_line_width=1, axes_color='black', facecolor='white', point_size=100, cmap='viridis', fontsize_legend=24, alpha_trans=1, plot_titel='Trajectory of the disease progression')
Find trajectories using Diffusion Maps and visualize the trajectory plot.
Parameters
- adataAnnData
Annotated data matrix containing EMD, annotations, and other necessary data.
- n_evecsint, optional
Number of embedding vectors, by default 2.
- epsilonfloat or str, optional
Method for choosing the epsilon in diffusion maps, by default 1.
- alphafloat, optional
Normalization parameter in the bandwidth function, by default 0.5.
- knnint, optional
Number of nearest neighbors for constructing the kernel, by default 64.
- sample_colint, optional
Index of the column representing sample IDs in annotation data, by default 1.
- clustersstr, optional
Name of the column representing clusters/categories in annotation data, by default ‘status’.
- label_actbool, optional
Whether to label data points with sample IDs, by default False.
- colorslist, optional
List of colors for different categories, by default [‘#377eb8’, ‘#ff7f00’, ‘#e41a1c’].
- location_labelsstr, optional
Location of the legend labels, by default ‘center’.
- figsizetuple, optional
figsize, by default (12,12).
- font_sizeint, optional
Font size for labels and annotations, by default 24.
- axes_line_widthfloat, optional
Line width of the axes, by default 1.
- axes_colorstr, optional
Color of the axes lines, by default ‘black’.
- facecolorstr, optional
Background color of the figure, by default ‘white’.
- point_sizeint, optional
Size of the data points in the plot, by default 100.
- cmapstr, optional
Colormap for scatter plot, by default ‘viridis’.
- fontsize_legendint, optional
Font size of the legend, by default 24.
- alpha_transfloat, optional
Transparency level for data points, by default 1.
- plot_titlestr, optional
Title of the plot, by default “Trajectory of the disease progression”.
Returns
- None
Visualizes and saves the trajectory plot.