bio_volcano: Function to generate a volcano plot

In KatrionaGoldmann/BioOutputs: Visualisation of Biological Data

Function to generate a volcano plot

Description

This function generates a volcano plot from a top table using ggplot.

Usage

bio_volcano(
  toptable,
  fc.col = "log2FC",
  padj.col = NULL,
  padj.method = "fdr",
  padj.cutoff = 0.05,
  fc.cutoff = 1,
  marker.colour = c("grey60", "olivedrab", "salmon", "darkturquoise"),
  label.p.cutoff = NULL,
  label.row.indices = NULL,
  label.colour = "black",
  legend.labs = NULL,
  add.lines = TRUE,
  line.colour = "grey14",
  main = "Volcano Plot",
  xlims = NULL,
  ylims = NULL
)

Arguments

toptable	A data frame containing p value and fold change columns for parameters compared across multiple groups. The p value column should be named "pvalue".
fc.col	The column name which stores the fold change. Should be in the log2 format (default="log2FC")
padj.col	The column which contains adjusted p-values. If NULL adjusted pvalues will be calculated
padj.method	correction method. Options include: c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"). Default="fdr
padj.cutoff	The cutoff for adjusted pvalues. This adds a horizontal line of significance (default=NULL)
fc.cutoff	The log2(fold change) significance cut-off (default=1)
marker.colour	Character vector of four colours to map to the volcano plot. In the order non-significanct, fold-change significant, pvalue significant, significant in fold-change and pvalues (default=c("grey60", "olivedrab", "salmon", "darkturquoise"))
label.p.cutoff	The cutoff for adjusted pvalues for labelling (default=NULL). Not recommended if many significant rows.
label.row.indices	Indices of rows to be labelled (default=NULL)
label.colour	Colour of labels (default="black")
legend.labs	A character vector for theThe legend label names (default=c("Not Significant", "FC>fc.cutoff", "Padj<padj.cutoff", "FC>fc.cutoff& Padj<padj.cutoff"))
add.lines	Whether to add dashed lines at fc.cutoff and padj.cutoff (default=TRUE)
line.colour	The color of dashed significance lines (default="grey14")
main	Plot title
xlims, ylims	The plot limits

Examples

bio_volcano(toptable)

KatrionaGoldmann/BioOutputs documentation built on May 21, 2022, 1:24 p.m.