c2v.pl.volcano#
- c2v.pl.volcano(pvals=None, logfcs=None, names=None, adj_p=False, lg_p=True, ax=None, return_fig=False, draw_p_threshold=True, pval_threshold=0.05, draw_logfc_threshold=True, logfc_threshold=1.0, n_highlite=5, highlite_names=None, background_scatter_kws=None, lines_kws=None, scatters_kws=None, pval_line_kws=None, pval_scatter_kws=None, logfc_scatter_kws=None, logfc_scatter_kws_left=None, logfc_scatter_kws_right=None, logfc_line_kws=None, logfc_line_kws_left=None, logfc_line_kws_right=None, pval_logfc_scatter_kws=None, pval_logfc_scatter_kws_left=None, pval_logfc_scatter_kws_right=None, highlite_scatter_kws=None, highlite_scatter_kws_right=None, highlite_scatter_kws_left=None, text_kws=None, text_kws_right=None, text_kws_left=None, xlim=None, ylim=None, title='Volcano plot', xlabel=None, ylabel=None, grid=True, rasterize=True, show=True, figsize=None)#
Draw a volcano using provided p-values and logFCs.
- Parameters:
- pvals pd.Series | list
P-values for each gene.
- logfcs pd.Series | list
Log2 fold changes for each gene.
- names pd.Series | list | None, optional
Gene names corresponding to p-values and logFCs. If None, indices are used (if provided). If not provided, no gene names are shown. Default is None.
- adj_p bool, optional
Whether p-values are adjusted (used to label the Y-axis). Default is False.
- lg_p bool, optional
Whether to use -log10(p) scale. If False, the function expects -log10(p) in pvals. Default is True.
- ax matplotlib.axes.Axes | None, optional
Axes to draw the volcano on. Default is None.
- return_fig bool, optional
Whether to return the figure. Default is False.
- draw_p_threshold bool, optional
Whether to draw the p-value threshold line. Default is True.
- pval_threshold float | None, optional
P-value threshold for significance. Default is 0.05.
- draw_logfc_threshold bool, optional
Whether to draw the logFC threshold lines. Default is True.
- logfc_threshold float | None, optional
Log2 fold change threshold for significance. Default is 1.0.
- n_highlite int, optional
Number of top genes to highlight from each side. Default is 5.
- highlite_names list | None, optional
List of gene names to highlight in addition to top-DE genes. Default is None.
- background_scatter_kws dict | None, optional
Keyword arguments for background (p > pval_threshold and |logFC| < logfc_threshold) scatter plot. Default is None.
- lines_kws dict | None, optional
Keyword arguments for all lines. Default is None.
- scatters_kws dict | None, optional
Keyword arguments for all scatters. Default is None.
- pval_line_kws dict | None, optional
Keyword arguments for p-value threshold line. Default is None.
- pval_scatter_kws dict | None, optional
Keyword arguments for p-value threshold scatter. Default is None.
- logfc_scatter_kws dict | None, optional
Keyword arguments for logFC threshold scatter. Default is None.
- logfc_scatter_kws_left dict | None, optional
Keyword arguments for logFC threshold scatter on the left side. Default is None.
- logfc_scatter_kws_right dict | None, optional
Keyword arguments for logFC threshold scatter on the right side. Default is None.
- logfc_line_kws dict | None, optional
Keyword arguments for logFC threshold line. Default is None.
- logfc_line_kws_left dict | None, optional
Keyword arguments for logFC threshold line on the left side. Default is None.
- logfc_line_kws_right dict | None, optional
Keyword arguments for logFC threshold line on the right side. Default is None.
- pval_logfc_scatter_kws dict | None, optional
Keyword arguments for p-value and logFC threshold scatter. Default is None.
- pval_logfc_scatter_kws_left dict | None, optional
Keyword arguments for p-value and logFC threshold scatter on the left side. Default is None.
- pval_logfc_scatter_kws_right dict | None, optional
Keyword arguments for p-value and logFC threshold scatter on the right side. Default is None.
- highlite_scatter_kws dict | None, optional
Keyword arguments for highlite scatter plot. Default is None.
- highlite_scatter_kws_right dict | None, optional
Keyword arguments for highlite scatter plot on the right side. Default is None.
- highlite_scatter_kws_left dict | None, optional
Keyword arguments for highlite scatter plot on the left side. Default is None.
- text_kws dict | None, optional
Keyword arguments for text. Default is None.
- text_kws_right dict | None, optional
Keyword arguments for text on the right side. Default is None.
- text_kws_left dict | None, optional
Keyword arguments for text on the left side. Default is None.
- xlim tuple[float, float] | None, optional
x-axis limits. Default is None.
- ylim tuple[float, float] | None, optional
y-axis limits. Default is None.
- title str | None, optional
Title of the plot. Default is None.
- xlabel str | None, optional
x-axis label. Default is None.
- ylabel str | None, optional
y-axis label. Default is None.
- grid bool, optional
Whether to draw grid lines. Default is True.
- rasterize bool, optional
Whether to rasterize the plot. Default is True.
- show bool, optional
Whether to show the plot. Default is True.
- figsize tuple[float, float] | None, optional
Figure size. Default is None.
- Return type:
Figure|Axes|None- Returns:
fig : matplotlib.figure.Figure Figure object if return_fig is True.