tirank.Visualization.DEG_volcano

tirank.Visualization.DEG_volcano(savePath, fc_threshold=2, Pvalue_threshold=0.05, do_p_adjust=True, top_n=5)[source]

Generates and saves a volcano plot for DEG results.

This function loads the ‘All DEGs dataframe.csv’ file, creates a volcano plot (Log2(FoldChange) vs -Log10(P-value)), colors genes based on significance thresholds, and annotates the top N most significant up- and down-regulated genes.

Parameters:

  • savePath (str) – The base directory containing the ‘3_Analysis’ subfolder.

  • fc_threshold (float, optional) – Fold-change threshold for coloring and vertical lines. Defaults to 2.

  • Pvalue_threshold (float, optional) – P-value threshold for coloring and the horizontal line. Defaults to 0.05.

  • do_p_adjust (bool, optional) – If True, use adjusted p-values for the Y-axis and filtering. If False, use raw p-values. Defaults to True.

  • top_n (int, optional) – The number of top up- and down-regulated genes to annotate. Defaults to 5.

Returns:

None