splicejac.plot.jacobian_visual
plotting resources for Jacobian and eigenvalues visualization
Module Contents
Functions
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Plot the inferred gene-gene interaction matrices of each cell state |
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Plot the eigenvalues of each cell state |
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Plot the eigenspectrum of a cell state on a matplotlib axis |
- splicejac.plot.jacobian_visual.visualize_jacobian(adata, panel_height=3, panel_length=3.5, pan_per_row=4, fontsize=10, cmap='RdBu_r', showfig=None, savefig=None, format='pdf')
Plot the inferred gene-gene interaction matrices of each cell state
- adata: ~anndata.AnnData
count matrix
- panel_height: float (default: 3)
height of each panel (in inches)
- panel_length: float (default: 3.5)
length of each panel (in inches)
- pan_per_row: int (default: 4)
number of panels per row
- fontsize: int (default: 10)
fontsize for labels
- cmap: str (default: ‘RdBu_r’)
colormap for Jacobian visualization. Accepted colormaps ca be found at: https://matplotlib.org/stable/tutorials/colors/colormaps.html
- 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
- splicejac.plot.jacobian_visual.eigen_spectrum(adata, panel_height=4, panel_length=4, pan_per_row=4, fontsize=10, show_frac=True, loc='lower right', show_zero=True, showfig=None, savefig=None, format='pdf')
Plot the eigenvalues of each cell state
- adata: ~anndata.AnnData
count matrix
- panel_height: float (default: 3)
height of each panel (in inches)
- panel_length: float (default: 3.5)
length of each panel (in inches)
- pan_per_row: int (default: 4)
number of panels per row
- fontsize: int (default: 10)
fontsize for labels
- show_frac: Bool (default: True)
show legend with fraction of positive eigenvalues
- loc: str (default: ‘lower right’)
location of legend. Accepted legend positions can be found at: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.legend.html
- show_zero: Bool (default: True)
plot horizontal line to highlight change of sign
- 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
- splicejac.plot.jacobian_visual.spectrum_plot(ax, v, title, show_frac=True, loc='lower right', show_zero=True, fontsize=10)
Plot the eigenspectrum of a cell state on a matplotlib axis
- ax: pyplot axis
axis to plot
- v: ~numpy.ndarray
ranked real components of eigenvalues
- title: str
title of plot
- show_frac: Bool (default: True)
show legend with fraction of positive eigenvalues
- loc: str (default: ‘lower right’)
location of legend. Accepted legend positions can be found at: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.legend.html
- show_zero: Bool (default: True)
plot horizontal line to highlight change of sign
- fontsize: int (default: 10)
fontsize for labels
None