plotCounts {DESeq2} | R Documentation

## Plot of normalized counts for a single gene

### Description

Normalized counts plus a pseudocount of 0.5 are shown by default.

### Usage

    plotCounts(dds, gene, intgroup = "condition", normalized = TRUE,
      transform = TRUE, main, xlab = "group", returnData = FALSE,
      replaced = FALSE, pc, ...)

### Arguments

`dds` | a `DESeqDataSet`
`gene` | a character, specifying the name of the gene to plot
`intgroup` | interesting groups: a character vector of names in `colData(x)` to use for grouping. Must be factor variables. If you want to plot counts over numeric, choose `returnData=TRUE`
`normalized` | whether the counts should be normalized by size factor (default is TRUE)
`transform` | whether to have log scale y-axis or not. defaults to TRUE
`main` | as in 'plot'
`xlab` | as in 'plot'
`returnData` | should the function only return the data.frame of counts and covariates for custom plotting (default is FALSE)
`replaced` | use the outlier-replaced counts if they exist
`pc` | pseudocount for log transform
`...` | arguments passed to plot

### Examples

    dds <- makeExampleDESeqDataSet()
    plotCounts(dds, "gene1")

[Package DESeq2 version 1.20.0 Index]