splicejac.plot.signaling
functions to plot signaling strength and changes
Module Contents
Functions
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Scatterplot of genes based on their signaling scores in a cell state |
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Scatterplot of the gene signaling changes between two cell states |
- splicejac.plot.signaling.plot_signaling_hubs(adata, cluster, fontsize=10, top_genes=5, line_width=0.5, show_top_genes=True, criterium='weights', cmap='Reds', showfig=None, savefig=None, format='pdf', figsize=(3.5, 3))
Scatterplot of genes based on their signaling scores in a cell state
Parameters of matplotlib.pyplot.scatter are explained at: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.scatter.html
- adata: ~anndata.AnnData
count matrix
- cluster: str
cell state
- fontsize: int (default=10)
fontsize of figure
- top_genes: int (default=5)
number of top genes to label with gene name
- line_width: float (default=0.5)
line width for scatter plot
- show_top_genes: Bool (default=True)
if True, annotate the top genes
- criterium: str (default=’weights’)
criterium to rank top genes. “weights” ranks genes based on the weighted edges of the cell state GRN, “edges” ranks genes based on the number of edges
- cmap: str (default: ‘Reds’)
the pyplot colormap for the scatter plot. A list of accepted color maps can 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’)
format of saved figure
- figsize: tuple (default:(3.5,3))
size of figure
None
- splicejac.plot.signaling.plot_signaling_change(adata, cluster1, cluster2, fontsize=10, top_genes=10, show_top_genes=True, criterium='weights', logscale_fc=True, x_shift=0.05, y_shift=0.05, cmap='coolwarm', line_width=0.5, showfig=None, savefig=None, format='pdf', figsize=(3.5, 3))
Scatterplot of the gene signaling changes between two cell states
- adata: ~anndata.AnnData
count matrix
- cluster1: str
first cell state
- cluster2: str
second cell state
- fontsize: int (default=10)
fontsize of figure
- top_genes: int (default=10)
number of top genes to label with gene name
- show_top_genes: Bool (default=True)
if True, annotate the top genes
- criterium: str (default=’weights’)
criterium to rank top genes. “weights” ranks genes based on the weighted edges of the cell state GRN, “edges” ranks genes based on the number of edges
- logscale_fc: Bool (default=True)
if True, rescale signaling change scores to logarithmic scale
- x_shift: float (default: 0.05)
displacement on x-axis for gene annotations
- y_shift: float (default: 0.05)
displacement on y-axis for gene annotations
- cmap: str (default: ‘coolwarm’)
the pyplot colormap for the scatter plot. A list of accepted color maps can be found at: https://matplotlib.org/stable/tutorials/colors/colormaps.html
- line_width: float (default=0.5)
line width for scatter plot
- 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’)
format of saved figure
- figsize: tuple (default:(3.5,3))
size of figure
None