Create a labeled MA plot

This function creates an MA plot from a data.frame containing DE analysis results.

Usage

plotMA.label(
  res,
  fdr.thres = 0.01,
  fc.thres = 0,
  fc.lim = NULL,
  lab.genes = NULL,
  opacity = 0.8,
  tolower.cols = c("SYMBOL", "ALIAS")
)

Arguments

res

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

fdr.thres

False discovery rate (FDR) threshold

fc.thres

log2FoldChange threshold

fc.lim

y-axis limits

lab.genes

genes to label on MA plot

opacity

point opacity between 0 and 1

tolower.cols

column names that will be converted to lower case

Value

ggplot handle

Examples

# make mock results df
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)
       )

plotMA.label(res, lab.genes = c("gene1", "gene2"))