decoupler.plot_volcano
- decoupler.plot_volcano(logFCs, pvals, contrast, name=None, net=None, top=5, source='source', target='target', weight='weight', sign_thr=0.05, lFCs_thr=0.5, sign_limit=None, lFCs_limit=None, color_pos='#D62728', color_neg='#1F77B4', color_null='gray', figsize=(7, 5), dpi=100, ax=None, return_fig=False, save=None)
Plot logFC and p-values. If name and net are provided, it does the same for the targets of a selected source.
- Parameters:
- logFCsDataFrame
Data-frame of logFCs (contrasts x features).
- pvalsDataFrame
Data-frame of p-values (contrasts x features).
- contraststr
Name of the contrast (row) to plot.
- namestr, None
Name of the source to plot. If None, plot classic volcano (without subsetting targets).
- netDataFrame, None
Network dataframe. If None, plot classic volcano (without subsetting targets).
- topint
Number of top differentially expressed features.
- sourcestr
Column name in net with source nodes.
- targetstr
Column name in net with target nodes.
- weightstr, None
Column name in net with weights. If none, set to None.
- sign_thrfloat
Significance threshold for p-values.
- lFCs_thrfloat
Significance threshold for logFCs.
- sign_limitfloat
Limit of p-values to plot in -log10.
- lFCs_limitfloat
Limit of logFCs to plot in absolute value.
- color_pos: str
Color to plot significant positive genes.
- color_neg: str
Color to plot significant negative genes.
- color_null: str
Color to plot rest of the genes.
- figsizetuple
Figure size.
- dpiint
DPI resolution of figure.
- axAxes, None
A matplotlib axes object. If None returns new 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.