splicejac.plot.grn_comparison
functions to quantitatively compare GRNs across cell states
Module Contents
Functions
|
Plot a heatmap of pairwise similarities between GRNs of different cell states |
|
Plot the pairwise GRN similarity between consecitive cell states along a transition |
- splicejac.plot.grn_comparison.plot_grn_comparison(adata, score='AUPRC', edges='all', cmap='Reds', title=False, fontsize=10, showfig=None, savefig=None, format='pdf', figsize=(5, 4))
Plot a heatmap of pairwise similarities between GRNs of different cell states
- adata: ~anndata.AnnData
count matrix
- score: str (default: ‘AUPRC’)
metric to use, choose between ‘AUROC’ and ‘AUPRC’
- edges: str (default: ‘all’)
which edges to consider for similarity, choose between ‘all’, ‘positive’, ‘negative’
- cmap: pyplot colormap (default=’Reds’)
colormap to use. A list of accepted colormaps can be found at: https://matplotlib.org/stable/tutorials/colors/colormaps.html
- title: str or Bool (default=’False’)
plot title, must be provided as a string
- fontsize: int (default: 10)
fontsize for 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
- figsize: tuple (default: (5,4))
size of figure
None
- splicejac.plot.grn_comparison.adjecent_grn_score(adata, path, score='AUPRC', edges='all', loc='best', fontsize=10, color='r', errorline_color='b', elinewidth=1, showfig=None, savefig=None, format='pdf', figsize=(5, 3))
Plot the pairwise GRN similarity between consecitive cell states along a transition
- adata: ~anndata.AnnData
count matrix
- path: list
list of cell states along the transition path
- score: str (default: ‘AUPRC’)
metric to use, choose between ‘AUROC’ and ‘AUPRC’
- edges: str (default: ‘all’)
which edges to consider for similarity, choose between ‘all’, ‘positive’, ‘negative’
- loc: str (default=’best’)
location of legend. Details on legend location can be found at: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.legend.html
- fontsize: int (default: 10)
fontsize for figure
- color: str (default: ‘r’)
color of plot. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- errorline_color: str (default: ‘b’)
color of deviation bars. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- elinewidth: float (default: 1)
width of deviation bars
- 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
- figsize: tuple (default: (5,3))
size of figure
None