omicverse.pl.volcano

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omicverse.pl.volcano#

omicverse.pl.volcano(result, pval_name='qvalue', fc_name='log2FC', pval_max=None, FC_max=None, figsize=(4, 4), title='', titlefont={'size': 14, 'weight': 'normal'}, up_color='#e25d5d', down_color='#7388c1', normal_color='#d7d7d7', up_fontcolor='#e25d5d', down_fontcolor='#7388c1', normal_fontcolor='#d7d7d7', legend_bbox=(0.8, -0.2), legend_ncol=2, legend_fontsize=12, show_thresholds=True, threshold_color='0.55', threshold_linewidth=0.8, threshold_linestyle='--', show_normal_in_legend=True, plot_genes=None, plot_genes_num=10, plot_genes_fontsize=10, ticks_fontsize=None, pval_threshold=0.05, fc_max=1.5, fc_min=-1.5, label_fontsize=None, ax=None)[source]#

Create a volcano plot for differential expression analysis.

Parameters:

  • result (pd.DataFrame) – Differential-expression result table containing at least p-value, fold-change, and sig classification columns.

  • pval_name (str) – Column name of adjusted p-values or q-values.

  • fc_name (str) – Column name of log fold-change values.

  • pval_max (float or None) – Optional y-axis upper bound in transformed p-value scale.

  • FC_max (float or None) – Optional x-axis absolute range cap.

  • figsize (tuple) – Figure size passed to matplotlib.

  • title (str) – Plot title.

  • titlefont (dict) – Font dict for title/axis labels.

  • up_color (str) – Point color for up-regulated genes.

  • down_color (str) – Point color for down-regulated genes.

  • normal_color (str) – Point color for non-significant genes.

  • up_fontcolor (str) – Label color for up-regulated genes.

  • down_fontcolor (str) – Label color for down-regulated genes.

  • normal_fontcolor (str) – Label color for non-significant genes.

  • legend_bbox (tuple) – Legend anchor position.

  • legend_ncol (int) – Number of legend columns.

  • legend_fontsize (int) – Legend font size.

  • show_thresholds (bool) – Draw the fold-change and p-value guide lines. False omits them.

  • threshold_color (str (default: '0.55')) – Style of those guides. The default is a thin grey dash; they used to be fixed at 2 pt solid black, which reads as content rather than as an annotation — especially in a small panel.

  • threshold_linewidth (float (default: 0.8)) – Style of those guides. The default is a thin grey dash; they used to be fixed at 2 pt solid black, which reads as content rather than as an annotation — especially in a small panel.

  • threshold_linestyle (str (default: '--')) – Style of those guides. The default is a thin grey dash; they used to be fixed at 2 pt solid black, which reads as content rather than as an annotation — especially in a small panel.

  • show_normal_in_legend (bool) – Include the non-significant count in the legend. It is the majority of the points, so leaving it out left the grey cloud unexplained.

  • plot_genes (list or None) – Explicit gene list to annotate.

  • plot_genes_num (int) – Number of top genes automatically annotated when plot_genes is None.

  • plot_genes_fontsize (int) – Font size for annotated gene labels.

  • ticks_fontsize (int or None) – Tick label font size. When None follows rcParams['xtick.labelsize'].

  • pval_threshold (float) – Significance threshold used to define highlighted genes.

  • fc_max (float) – Positive fold-change cutoff.

  • fc_min (float) – Negative fold-change cutoff.

  • label_fontsize (float or None) – Font size of the x/y axis labels. When None follows rcParams['axes.labelsize'] so the labels match surrounding panels instead of the fixed title font size.

  • ax (matplotlib.axes.Axes or None) – Existing axes object to draw on.

Returns:

Axes containing the volcano plot.

Return type:

matplotlib.axes.Axes

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