This function creates a volcano plot with optional interactivity via ggiraph. Code from https://github.com/YuLab-SMU/ivolcano
Usage
ivolcano(
data,
logFC_col = "logFC",
pval_col = "adj.P.Val",
gene_col = "gene",
title = "",
interactive = TRUE,
onclick_fun = NULL,
pval_cutoff = 0.05,
logFC_cutoff = 1,
top_n = 10,
label_mode = "separate",
fontface = "italic",
label_sig_only = TRUE,
threshold_line = list(color = "black", linetype = "dashed", linewidth = 0.5),
sig_colors = c(Up = "red", Down = "blue", Not_Significant = "grey70"),
size_by = "none"
)Arguments
- data
Input data frame.
- logFC_col
Column name storing log fold change.
- pval_col
Column storing adjusted P value.
- gene_col
Column storing gene names.
- title
Plot title.
- interactive
Whether to use ggiraph.
- onclick_fun
Optional function for onclick events.
- pval_cutoff
FDR threshold.
- logFC_cutoff
LogFC threshold.
- top_n
Number of labels to draw.
- label_mode
Label mode.
- fontface
Label font face.
- label_sig_only
Whether to only label significant genes.
- threshold_line
Line settings for cutoff.
- sig_colors
Colors for Up/Down/Not_Significant.
- size_by
Optional scaling variable.