Create a static labeled Volcano plot

This function creates a static ggplot Volcano plot from a data.frame containing DE analysis results. Mirrors plotVolcano.label_ly but renders with ggplot2 for use in downloads.

Usage

plotVolcano.label(
  res,
  fdr.thres = 0.1,
  fc.thres = 0,
  y.axis.lim = NULL,
  fc.lim = c(-4, 4),
  lab.genes = NULL,
  tolower.cols = c("SYMBOL", "ALIAS"),
  color_by = c("baseMean", "significance"),
  colorscale = "viridis",
  alpha = 0.6,
  pvalue_padj_switch = c("pvalue", "padj")
)

Arguments

res

data.frame with DE analysis results. Must contain "pvalue", "padj", "baseMean" & "log2FoldChange" columns

fdr.thres

False discovery rate (FDR) threshold

fc.thres

log2FoldChange threshold

y.axis.lim

y-axis limits for negative log10 p-values

fc.lim

x-axis limits

lab.genes

genes to label on plot

tolower.cols

column names that will be converted to lower case

color_by

variable to color points by ('baseMean' or 'significance')

colorscale

ggplot-compatible continuous colorscale name (viridis option), only used when color_by='baseMean'

alpha

point opacity between 0 and 1

pvalue_padj_switch

Switches between having the y-axis display raw or adjusted p-values. Significance is always determined by adjusted values.

Value

ggplot handle

Examples

n_genes <- 100
res <- data.frame(
         baseMean = runif(n_genes, 10, 1000),
         log2FoldChange = rnorm(n_genes, 0, 2),
         lfcSE = runif(n_genes, 0.1, 0.5),
         stat = rnorm(n_genes, 0, 3),
         pvalue = runif(n_genes, 0, 1),
         padj = runif(n_genes, 0, 1),
         symbol = paste0("GENE", 1:n_genes),
         row.names = paste0("gene", 1:n_genes)
       )

plotVolcano.label(res, lab.genes = c("gene1", "gene2"))
#> Error in plotVolcano.label(res, lab.genes = c("gene1", "gene2")): could not find function "plotVolcano.label"