sc_toolbox.plot.volcano_plot#

sc_toolbox.plot.volcano_plot(table, fdr_thresh=None, log_fc_thresh=0, adj_p_val='adj_p_val', log_fc='avg_logFC', gene='gene', sig_col='tab:orange', col='tab:blue', figsize=(8, 6), save=None)[source]#

Scatter plot of differential gene expression results generated by diffxpy

Parameters:

  • table – diffxpy generated table of results

  • fdr_thresh (Optional[float]) – -log(FDR) threshold for labeling genes. If set to None, we will consider the 99th percentile of -log(FDR) values the threshold.

  • log_fc_thresh (float) – absolute(log_fc) threshold for labeling genes.

  • adj_p_val (str) – Label of the adjusted p value, these are considered FDRs

  • log_fc (str) – Label of the log fold change

  • gene (str) – Label of column with gene names

  • col (str) – Color of dots

  • sig_col (str) – Colour of dots surpassing defined FDR threshold

  • figsize (Tuple[int, int]) – Size of the figure as specified in matplotlib

  • save – Path to save the plot to

Example

../../_images/diffxpy_volcano.png