metachat.pl.plot_DEG_volcano

metachat.pl.plot_DEG_volcano(deg_result, name_col='names', logfc_col='logfoldchanges', pval_col='pvals_adj', logfc_thresh=1.0, pval_thresh=0.05, neglog10_cap=50.0, pointsize_min=5.0, pointsize_max=30.0, label_thresh_neglog10=10.0, label_fontsize=6, figsize=(5, 5), cbar_orientation='horizontal', cbar_pad=0.2, title='Volcano Plot', show_labels=True, ax=None, plot_savepath=None)

Plot a volcano plot from differential MCC results.

This function visualizes log2 fold changes versus statistical significance (-log10 adjusted p-values) to highlight up- and down-regulated genes.

Parameters

deg_resultpandas.DataFrame

DataFrame containing differential MCC results.

name_colstr, default=’names’

Column name for gene or feature names.

logfc_colstr, default=’logfoldchanges’

Column name for log2 fold changes.

pval_colstr, default=’pvals_adj’

Column name for adjusted p-values.

logfc_threshfloat, default=1.0

Threshold for absolute log2 fold change used to draw vertical reference lines.

pval_threshfloat, default=0.05

Threshold for adjusted p-value used to draw a horizontal reference line.

neglog10_capfloat, default=50.0

Cap for -log10(p-value) to avoid extreme values distorting visualization.

pointsize_minfloat, default=5.0

Minimum scatter point size.

pointsize_maxfloat, default=30.0

Maximum scatter point size.

label_thresh_neglog10float, default=10.0

Threshold of -log10(p-value) above which gene labels are annotated.

label_fontsizeint, default=6

Font size for gene labels.

figsizetuple of float, default=(5, 5)

Figure size (width, height) in inches.

cbar_orientation{‘horizontal’, ‘vertical’}, default=’horizontal’

Orientation of the colorbar.

cbar_padfloat, default=0.2

Padding distance between colorbar and axis.

titlestr, default=’Volcano Plot’

Title of the figure.

show_labelsbool, default=True

Whether to show text labels for significant genes.

axmatplotlib.axes.Axes, optional

Existing Matplotlib axis to draw on. If None, a new figure and axis are created.

plot_savepathstr, optional

File path to save the figure (e.g. 'results/volcano_plot.pdf'). The format is inferred from the file extension. If None, the figure is shown interactively.

Returns

axmatplotlib.axes.Axes

Matplotlib axis object containing the rendered volcano plot.

Notes

• Points are colored by log2 fold change using a diverging colormap.

• Vertical and horizontal dashed lines represent significance thresholds.

• Extreme -log10(p-values) are capped at neglog10_cap to maintain scale.