splicejac.plot.grn_plots
plotting resources for GRN visualization
Module Contents
Functions
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Plot the GRN with positive and negative interactions |
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Plot the gene regulatory network of a cluster |
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Plot the differential network between two cell states |
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Plot the top differential interactions between two cell states |
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Plot the conserved network between two cell states |
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Plot the top conserved interactions between two cell states |
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Calculate gene expression mean based on quantile selection |
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normalize the gene expression data |
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Compute coordinates along a unit circle for GRN node positions |
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select gene-gene interactions for genes in the genelist |
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Plot a reduced GRN including the top DEG of the starting cluster and the top transition genes |
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Plot the reduced GRN of transition genes involved in different cell state transitions |
- splicejac.plot.grn_plots.plot_grn(G, node_size=200, edge_width=1, font_size=8, adata=None, node_color='centrality', cluster_name=None, pos_style='spring', base_node_size=300, diff_node_size=600, pos_edge_color='b', neg_edge_color='r', arrowsize=10, arrow_alpha=0.75, conn_style='straight', colorbar=True, fontweight='normal')
Plot the GRN with positive and negative interactions
- G: networkx graph object
network to plot
- node_size: int or str (default: 200)
size of nodes. If node_size=’expression’, the node size is scaled based on gene expression. Otherwise, node_size can be a fixed integer
- edge_width: float (default: 1)
width of connection arrows
- fontsize: int (default: 10)
fontsize for node labels.
- adata: ~anndata.AnnData or None (default: None)
count matrix, must be provided if node_size == ‘expression’
- node_color: str (default: ‘centrality’)
color of nodes. If node_color=’centrality’, the color is based on the node centrality. Otherwise, a matplotlib color name can be provided. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- cluster_name: str or None (default: None)
name of considered cluster (must be provided if node_size=’expression’)
- pos_style: str (default: ‘spring’)
position of nodes. The options are ‘spring’ and ‘circle’. ‘spring’ uses the networkx spring position function, whereas ‘circle’ arranges the nodes in a circle.
- base_node_size: float (default: 300)
Minimum node size (used if node_size=’expression’)
- diff_node_size: float (default: 600)
difference between minimum and maximal node size (used if node_size=’expression’)
- pos_edge_color: str (default: ‘b’)
color for positive regulation arrow. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- neg_edge_color: str (default: ‘r’)
color for negative regulation arrow. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- arrowsize: float (default: 10)
size of interaction arrows
- arrow_alpha: float (default: 0.75)
shading of interaction arrows in [0,1]
- conn_style: str (default: ‘straight’)
style of interaction arrows. The admissible styles for networkx graphs can be found at: https://networkx.org/documentation/stable/reference/generated/networkx.drawing.nx_pylab.draw_networkx_edges.html
- colorbar: Bool (default: True)
if True, show colorbar (required if node_size=’expression’)
- fontweight: str (default: ‘normal’)
style of text. Can select ‘bold’ for bold text.
None
- splicejac.plot.grn_plots.visualize_network(adata, cluster_name, genes=None, cc_id=0, node_size='expression', edge_width='weight', font_size=10, plot_interactive=True, weight_quantile=0.5, node_color='centrality', pos_style='spring', title=True, base_node_size=300, diff_node_size=600, pos_edge_color='b', neg_edge_color='r', arrowsize=10, arrow_alpha=0.75, conn_style='straight', colorbar=True, fontweight='normal', showfig=None, savefig=None, format='pdf', figsize=(4, 3))
Plot the gene regulatory network of a cluster
- adata: ~anndata.AnnData
count matrix
- cluster_name: str
cell state
- genes: list (default: None)
list of genes to include. If None, all genes are included
- cc_id: int (default: 0)
connected component of the GRN to plot
- node_size: int or str (default: 200)
size of nodes. If node_size=’expression’, the node size is scaled based on gene expression. Otherwise, node_size can be a fixed integer
- edge_width: float (default: 1)
width of connection arrows
- fontsize: int (default: 10)
fontsize for node labels.
- plot_interactive: Bool (default=True)
plot the GRN interactively in notebook of figure
- weight_quantile: float (default=0.5)
threshold to filter weak interactions between 0 and 1
- node_color: str (default: ‘centrality’)
color of nodes. If node_color=’centrality’, the color is based on the node centrality. Otherwise, a matplotlib color name can be provided. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- pos_style: str (default: ‘spring’)
position of nodes. The options are ‘spring’ and ‘circle’. ‘spring’ uses the networkx spring position function, whereas ‘circle’ arranges the nodes in a circle.
- title: Bool (default=True)
if True, plot title
- base_node_size: float (default: 300)
Minimum node size (used if node_size=’expression’)
- diff_node_size: float (default: 600)
difference between minimum and maximal node size (used if node_size=’expression’)
- pos_edge_color: str (default: ‘b’)
color for positive regulation arrow. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- neg_edge_color: str (default: ‘r’)
color for negative regulation arrow. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- arrowsize: float (default: 10)
size of interaction arrows
- arrow_alpha: float (default: 0.75)
shading of interaction arrows in [0,1]
- conn_style: str (default: ‘straight’)
style of interaction arrows. The admissible styles for networkx graphs can be found at: https://networkx.org/documentation/stable/reference/generated/networkx.drawing.nx_pylab.draw_networkx_edges.html
- colorbar: Bool (default: True)
if True, show colorbar (required if node_size=’expression’)
- fontweight: str (default: ‘normal’)
style of text. Can select ‘bold’ for bold text.
- 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_plots.diff_network(adata, cluster1, cluster2, genes=None, cc_id=0, node_size=500, edge_width='weight', font_size=10, weight_quantile=0.5, pos_style='spring', base_node_size=300, diff_node_size=600, pos_edge_color='b', neg_edge_color='r', arrowsize=10, arrow_alpha=0.75, conn_style='straight', colorbar=True, fontweight='normal', title=True, showfig=None, savefig=None, format='pdf', figsize=(3.5, 3))
Plot the differential network between two cell states
- adata: ~anndata.AnnData
count matrix
- cluster1: str
first cell state
- cluster2: str
second cell state
- genes: list (default: None)
list of genes to include. If None, all genes are included
- cc_id: int (default: 0)
connected component of the GRN to plot
- node_size: float (default=500)
size of nodes in the GRN
- edge_width: float or str (default=’weight’)
width of GRN edges. If edge_width=’weight’, the edge width is proportional to the interaction strength.
- fontsize: int (default: 10)
fontsize for figure.
- weight_quantile: float (default: 0.5)
threshold to filter weak interactions between 0 and 1
- pos_style: str (default: ‘spring’)
position of nodes. The options are ‘spring’ and ‘circle’. ‘spring’ uses the networkx spring position function, whereas ‘circle’ arranges the nodes in a circle.
- base_node_size: float (default: 300)
Minimum node size (used if node_size=’expression’)
- diff_node_size: float (default: 600)
difference between minimum and maximal node size (used if node_size=’expression’)
- pos_edge_color: str (default: ‘b’)
color for positive regulation arrow. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- neg_edge_color: str (default: ‘r’)
color for negative regulation arrow. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- arrowsize: float (default: 10)
size of interaction arrows
- arrow_alpha: float (default: 0.75)
shading of interaction arrows in [0,1]
- conn_style: str (default: ‘straight’)
style of interaction arrows. The admissible styles for networkx graphs can be found at: https://networkx.org/documentation/stable/reference/generated/networkx.drawing.nx_pylab.draw_networkx_edges.html
- colorbar: Bool (default: True)
if True, show colorbar (required if node_size=’expression’)
- fontweight: str (default: ‘normal’)
style of text. Can select ‘bold’ for bold text.
- title: Bool (default: True)
if True, plot title
- 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: (3.5,3))
size of figure
None
- splicejac.plot.grn_plots.diff_interactions(adata, cluster1, cluster2, top_int=10, loc='best', title=False, fontsize=10, legend_font=10, legend_col=1, showfig=None, savefig=None, format='pdf', figsize=(4, 5))
Plot the top differential interactions between two cell states
- adata: ~anndata.AnnData
count matrix
- cluster1: str
first cell state
- cluster2: str
second cell state
- top_int: int (default=10)
number of top changed interactions to plot
- 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
- title: Bool (default: False)
if True, plot title
- fontsize: int (default: 10)
fontsize for figure.
- legend_font: int (default: 10)
fontsize of legend
- legend_col: int (default: 1)
number of columns in legend
- 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: (4,5))
size of figure
None
- splicejac.plot.grn_plots.conserved_grn(adata, cluster1, cluster2, genes=None, cc_id=0, node_size=500, edge_width='weight', font_size=10, weight_quantile=0.5, pos_style='spring', title=True, base_node_size=300, diff_node_size=600, pos_edge_color='b', neg_edge_color='r', arrowsize=10, arrow_alpha=0.75, conn_style='straight', colorbar=True, fontweight='normal', showfig=None, savefig=None, format='pdf', figsize=(3.5, 3))
Plot the conserved network between two cell states
- adata: ~anndata.AnnData
count matrix
- cluster1: str
first cell state
- cluster2: str
second cell state
- genes: list or None (default: None)
list of genes to consider. If None, all genes are considered
- cc_id: int (default: 0)
connected component of the GRN to plot
- node_size: int (default: 500)
size of nodes in the GRN
- edge_width: str or int (default: ‘weight’)
width of GRN edges. If edge_width=’weight’, the edge width is proportional to the interaction strength.
- fontsize: int (default: 10)
fontsize for figure.
- weight_quantile: float (default: 0.5)
threshold to filter weak interactions between 0 and 1
- pos_style: str (default: ‘spring’)
position of nodes. The options are ‘spring’ and ‘circle’. ‘spring’ uses the networkx spring position function, whereas ‘circle’ arranges the nodes in a circle.
- title: Bool (default: True)
if True, plot title
- base_node_size: float (default: 300)
Minimum node size (used if node_size=’expression’)
- diff_node_size: float (default: 600)
difference between minimum and maximal node size (used if node_size=’expression’)
- pos_edge_color: str (default: ‘b’)
color for positive regulation arrow. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- neg_edge_color: str (default: ‘r’)
color for negative regulation arrow. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- arrowsize: float (default: 10)
size of interaction arrows
- arrow_alpha: float (default: 0.75)
shading of interaction arrows in [0,1]
- conn_style: str (default: ‘straight’)
style of interaction arrows. The admissible styles for networkx graphs can be found at: https://networkx.org/documentation/stable/reference/generated/networkx.drawing.nx_pylab.draw_networkx_edges.html
- colorbar: Bool (default: True)
if True, show colorbar (required if node_size=’expression’)
- fontweight: str (default: ‘normal’)
style of text. Can select ‘bold’ for bold text.
- 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: (3.5,3))
size of figure
None
- splicejac.plot.grn_plots.top_conserved_int(adata, cluster1, cluster2, top_int=10, title=False, fontsize=10, alpha=0.5, showfig=None, savefig=None, format='pdf', figsize=(4, 5))
Plot the top conserved interactions between two cell states
- adata: ~anndata.AnnData
count matrix
- cluster1: str
first cell state
- cluster2: str
second cell state
- top_int: int (default=10)
number of top chnaged interactions to plot
- title: Bool (default: False)
if True, plot title
- fontsize: int (default: 10)
fontsize for figure.
- alpha: float (default=0.5)
shading of bar 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’)
figure format
- figsize: tuple (default: (4,5))
size of figure
None
- splicejac.plot.grn_plots.robust_mean(X)
Calculate gene expression mean based on quantile selection
- X: ~numpy.ndarray`
array of gene expression values
- robust mean: ~numpy.ndarray`
array of mean gene expression
- splicejac.plot.grn_plots.NormalizeData(data)
normalize the gene expression data
- data: ~numpy.ndarray`
data array
- scaled: ~numpy.ndarray`
normalized data
- splicejac.plot.grn_plots.circle_pos(G)
Compute coordinates along a unit circle for GRN node positions
- G: networkx object
the networkx network
- pos: ~numpy.ndarray`
array of positions
- splicejac.plot.grn_plots.subset_jacobian(J, genes, genelist)
select gene-gene interactions for genes in the genelist
- J: ~numpy.ndarray
gene-gene interaction matrix
- genes: list
full list of genes
- genelist: list
list of selected genes
- B_subset: ~numpy.ndarray
reduced gene-gene interaction matrix
- splicejac.plot.grn_plots.core_GRN(adata, cluster1, cluster2, type_color=['orange', 'plum', 'yellowgreen'], pos_edge_color='b', neg_edge_color='r', node_size=500, node_alpha=0.5, arrowsize=10, arrow_alpha=0.75, conn_style='arc3, rad=0.1', node_font=8, legend=True, legend_font=10, legend_ncol=2, legend_loc='lower center', axis=False, xlim=[- 1.2, 1.2], ylim=None, showfig=None, savefig=None, format='pdf', figsize=(3, 3))
Plot a reduced GRN including the top DEG of the starting cluster and the top transition genes
- adata: ~anndata.AnnData
count matrix
- cluster1: str
first cell state
- cluster2: str
second cell state
- type_color: list (default=[‘orange’, ‘plum’, ‘yellowgreen’])
colors for nodes that are DEG, transition genes and both. A list of accepted colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- pos_edge_color: str (default: ‘b’)
color for positive regulation arrow. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- neg_edge_color: str (default: ‘r’)
color for negative regulation arrow. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- node_size: ‘int’ (default: 500)
size of nodes
- node_alpha: float (default: 0.5)
shading of nodes
- arrowsize: float (default: 10)
size of interaction arrows
- arrow_alpha: float (default: 0.75)
shading of interaction arrows in [0,1]
- conn_style: str (default: ‘arc3, rad=0.1’)
style of interaction arrows. The admissible styles for networkx graphs can be found at: https://networkx.org/documentation/stable/reference/generated/networkx.drawing.nx_pylab.draw_networkx_edges.html
- node_font: int (default: 8)
fontsize for node labels.
- legend: Bool (default=True)
if True, include legend
- legend_font: int (default=10)
font size for legend
- legend_ncol: int (default=2)
number of columns in legend
- legend_loc: str (default: ‘lower center’)
legend location. Details on legend location can be found at: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.legend.html
- axis: Bool (default=False)
if True, plot axes
- xlim: list (default=[-1.2, 1.2])
inteval on x-axis
- ylim: list or None (default=None)
inteval on y-axis
- 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.grn_plots.bif_GRN(adata, start, end, pos_edge_color='b', neg_edge_color='r', node_size=750, node_alpha=0.5, arrowsize=10, arrow_alpha=0.75, arrowstyle='arc3, rad=0.1', node_font=10, legend=True, legend_font=10, legend_ncol=3, legend_loc='lower center', axis=True, xlim=[- 1.2, 1.2], ylim=None, showfig=None, savefig=None, format='pdf', figsize=(6, 6))
Plot the reduced GRN of transition genes involved in different cell state transitions
- adata: ~anndata.AnnData
count matrix
- start: str
starting cell state
- end: list
list of ending cell states
- pos_edge_color: str (default: ‘b’)
color for positive regulation arrow. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- neg_edge_color: str (default: ‘r’)
color for negative regulation arrow. A full list of accepted named colors can be found at: https://matplotlib.org/stable/gallery/color/named_colors.html
- node_size: int (default: 500)
size of nodes
- node_alpha: float (default: 0.5)
shading of nodes
- arrowsize: float (default: 10)
size of interaction arrows
- arrow_alpha: float (default: 0.75)
shading of interaction arrows in [0,1]
- conn_style: str (default: ‘arc3, rad=0.1’)
style of interaction arrows. The admissible styles for networkx graphs can be found at: https://networkx.org/documentation/stable/reference/generated/networkx.drawing.nx_pylab.draw_networkx_edges.html
- node_font: int (default=8)
font size of node labels
- legend: Bool (default=True)
if True, include legend
- legend_font: int (default=10)
font size for legend
- legend_ncol: int (default=2)
number of columns in legend
- legend_loc: str (default=’lower center’)
legend location. Details on legend location can be found at: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.legend.html
- axis: Bool (default=False)
if True, plot axes
- xlim: list (default=[-1.2, 1.2])
inteval on x-axis
- ylim: list or None (default=None)
inteval on y-axis
- 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: (6,6))
size of figure
None