decoupler.plot_network
- decoupler.plot_network(net, obs=None, act=None, n_sources=5, n_targets=10, by_abs=True, node_size=0.5, label_size=5, s_cmap='RdBu_r', t_cmap='viridis', vcenter=False, c_pos_w='darkred', c_neg_w='darkblue', s_label='Enrichment score', t_label='Gene expression', layout='kk', figsize=(10, 10), dpi=150, return_fig=False, save=None)
Plot results of enrichment analysis as network.
- Parameters:
- netDataFrame
Network dataframe with
sourceandtargetcolumns (weightis optional).- obsNone, DataFrame
Input of enrichment analysis, needs to be a one row dataframe with targets as features. Used to filter net.
- actNone, DataFrame
Ouput of enrichment analysis, needs to be a one row dataframe with sources as features. Used to filter net.
- n_sourcesstr, list, int
Number of top sources to plot or list of source names.
- n_targetsstr, list, int
Number of top targets to plot or list of target names.
- by_absbool
Whether to consider the absolute value when sorting for
n_sourcesandn_targets.- node_sizefloat
Size of the nodes in the plot.
- label_sizeint
Size of the labels in the plot.
- s_cmapstr
Color or colormap to use to color sources.
- t_cmapstr
Color or colormap to use to color targets.
- vcenterbool
Whether to center colors around 0.
- c_pos_wstr
Color for edges with positive weights. If no weights are available, they are set to positive by default.
- c_neg_wstr
Color for edges with negative weights.
- s_labelstr
Label to place in the source colorbar.
- t_labelstr
Label to place in the target colorbar.
- layoutstr
Layout to use to order the nodes. Check
igraphdocumentation for more options.- figsizetuple
Figure size.
- dpiint
DPI resolution of figure.
- return_figbool
Whether to return a Figure object or not.
- savestr, None
Path to where to save the plot. Infer the filetype if ending on {
.pdf,.png,.svg}.
- Returns:
- figFigure, None
If return_fig, returns Figure object.