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Last data update: 2014.03.03

R: Plot of normalized counts for a single gene on log scale

plotCounts

R Documentation

Plot of normalized counts for a single gene on log scale

Description

Note: normalized counts plus a pseudocount of 0.5 are shown.

Usage

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

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
`normalized`	whether the counts should be normalized by size factor (default is TRUE)
`transform`	whether to present log2 counts (TRUE) or to present the counts on the log scale (FALSE, default)
`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
`...`	arguments passed to plot

Examples


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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(DESeq2)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DESeq2/plotCounts.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotCounts
> ### Title: Plot of normalized counts for a single gene on log scale
> ### Aliases: plotCounts
> 
> ### ** Examples
> 
> 
> dds <- makeExampleDESeqDataSet()
> plotCounts(dds, "gene1")
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>