splicejac.plot.instability
plotting functions for instability scores
Module Contents
Functions
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Plot the top transition genes between two cell states |
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Scatter plot to compare the spliceJAC transition scores with scanpy's DEG scores of the starting cell state |
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Scatter plots to compare spliceJAC's transition scores with scVelo's gene likelihood scores |
- splicejac.plot.instability.plot_trans_genes(adata, cluster1, cluster2, top_trans_genes=10, fontsize=10, color='r', alpha=0.5, showfig=None, savefig=None, format='pdf', figsize=(3, 3))
Plot the top transition genes between two cell states
- adata: ~anndata.AnnData
count matrix
- cluster1: str
starting cell state
- cluster2: str
final cell state
- top_trans_genes: int (default: 10)
top genes to include in the bar plot
- fontsize: int (default: 10)
fontsize for labels
- color: str (default: ‘r’)
color for bar plot. A list of named pyplot colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- alpha: float (default=0.5)
shading for bar plot in [0,1]
- 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: (3,3))
size of figure
None
- splicejac.plot.instability.scatter_scores(adata, cluster1, cluster2, fontsize=10, color='b', showfig=None, savefig=None, format='pdf', figsize=(3, 3))
Scatter plot to compare the spliceJAC transition scores with scanpy’s DEG scores of the starting cell state
- adata: ~anndata.AnnData
count matrix
- cluster1: str
starting cell state
- cluster2: str
final cell state
- fontsize: int (default: 10)
fontsize for labels
- color: str (default: ‘b’)
color for scatter plot. A list of named pyplot colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.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
- figsize: tuple (default: (3,3))
size of figure
None
- splicejac.plot.instability.compare_scvelo_scores(adata, annotate=True, top=5, color='b', panel_height=3, panel_length=3.5, pan_per_row=4, fontsize=10, showfig=None, savefig=None, format='pdf')
Scatter plots to compare spliceJAC’s transition scores with scVelo’s gene likelihood scores
- adata: ~anndata.AnnData
count matrix
- annotate: Bool (default=True)
if True, annotate the genes with highest sum of scores
- top: int (default=5)
number of top genes to annotate
- color: str (default: ‘b’)
color for scatter plot. A list of named pyplot colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- 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
- 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