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plotCounts

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")
DESeq2

Differential gene expression analysis based on the negative binomial distribution

v1.30.1
LGPL (>= 3)
Authors
Michael Love [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb]
Initial release

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