splicejac.plot.umap_scatter
functions for umap scatter plot visualization
Module Contents
Functions
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2D UMAP plot of the data |
- splicejac.plot.umap_scatter.umap_scatter(adata, ax=None, order=None, axis=False, fontsize=10, alpha=0.5, show_cluster_center=True, s=2, s_center=50, line_width=0.5, legens_pos=(0.5, 1.2), legend_loc='upper center', ncol=4, figsize=(4, 4), showfig=None, savefig=None, format='pdf')
2D UMAP plot of the data
Parameters of matplotlib.pyplot.scatter are explained at: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.scatter.html
- adata: ~anndata.AnnData
count matrix
- ax: pyplot axis or False (default: False)
if False generate a new figure
- order: list (default: None)
ordered list of cluster labels in the figure legend, if None the order is alphabetical
- axis: Bool (default: False)
if true draw axes, otherwise do not show axes
- fontsize: int (default: 10)
fontsize of axes and legend labels.
- alpha: float (default=0.5)
shading of individual cells between [0,1]
- show_cluster_center: Bool (default: True)
if True, plot the center of each cluster
- s: int (default=2)
size of individual cells
- s_center: int (default=50)
size of cluster center
- line_width: float (default=0.5)
line width for cluster centers
- legens_pos: tuple (default: (0.5, 1.2))
position of figure legend by axis coordinates. Details on legend location can be found at: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.legend.html
- legend_loc: str (default=’upper center’)
position of figure legend
- ncol: int (default: 4)
number of columns in the figure legend
- figsize: tuple (default: (4,4))
size of figure
- showfig: Bool or None (default: None)
if True, show the figure
- savefig: Bool or None (default: None)
if True, save the figure using the savefig path
- format: str (default: ‘pdf’)
figure format
None