pyscnet.Plotting¶
pyscnet.Plotting.geneHeatmap¶
Created on Thu May 9 11:32:32 2019 @author: mwu
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pyscnet.Plotting.geneHeatmap.
geneCorrelation
(gnetdata, gene, cell_clusterid, select_by, order_by=None, scale_data=True, save_as=None, figsize=None, **kwargs)[source]¶ - Parameters
gnetdata – Gnetdata object
gene – list, default None.
cell_clusterid – str, default None. cell with cell_clusterid will be selected
select_by – str, default None. key of filtering cells
order_by – str, default None. key of ordering cells
scale_data – bool, default True. whether or not scale the data
save_as – str, default None. filepath+filename
figsize – list, default None. a list of int defining figure size
kwargs – additional parameters passed to seaborn.clustermap()
- Returns
None
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pyscnet.Plotting.geneHeatmap.
geneDynamic
(gnetdata, gene, cell_clusterid, select_by, rolling=10, order_by=None, scale_data=True, save_as=None, colors=None, legend_size=None, **kwargs)[source]¶ - Parameters
gnetdata – Gnetdata object
gene – list, default None.
cell_clusterid – str, default None. cell with cell_clusterid will be selected
select_by – str, default None. key of filtering cells
order_by – str, default None. key of ordering cells
rolling – int, default 10. rolling window calculation
scale_data – bool, default True. whether or not scale the data
save_as – str, default None. filepath+filename
colors – list, default None. list of string denoting color map
legend_size – list, default None. specify legend size
kwargs – additional parameters passed to matplotlib.pyplot.plot()
- Returns
none
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pyscnet.Plotting.geneHeatmap.
geneHeatmap
(gnetdata, gene, cell_clusterid, select_by, order_by=None, scale_data=True, cmap='RdBu', save_as=None, **kwargs)[source]¶ - Parameters
gnetdata – Gnetdata object, default None
gene – list, default None.
cell_clusterid – str, default None. cell with cell_clusterid will be selected
select_by – str, default None. key of filtering cells
order_by – str, default None. key of ordering cells
scale_data – bool, default True. whether or not scale the data
cmap – str, default ‘RdBu’. string denoting colors in clustermap
save_as – str, default None. filepath+filename
kwargs – additional parameters passed to seaborn.clustermap()
- Returns
None
pyscnet.Plotting.show_net¶
Created on Thu May 9 11:32:32 2019 @author: mwu
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pyscnet.Plotting.show_net.
dynamic_netShow
(gnetdata, filename, node_size=50, html_size=['1200px', '1600px'])[source]¶ - Parameters
gnetdata – Gnetdata object
filename – str, save as filename
node_size – int, default 50.
html_size – list, default [“1200px”, “1600px”]
- Returns
None
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pyscnet.Plotting.show_net.
static_netShow
(gnetdata, filename, scale=4, figure_size=[20, 10], link_key='consensus', random_path=None, path_highlight=False, neighhours_highlight=False, start=None, **kwargs)[source]¶ - Parameters
gnetdata – Gnetdata object
filename – str, save as filename
scale – int, default 4.
figure_size – list, default [20, 10].
random_path – list, list of nodes for highlighting.
path_highlight – bool, default False.
neighhours_highlight – bool, default False.
start – str, default None.
kwargs – additional parameters passed to networkx.draw_networkx()
- Returns
None