Sparsity plot

Description

A simple plot of the concentration of counts in a single sample over the sum of counts per gene. Not technically the same as "sparsity", but this plot is useful diagnostic for datasets which might not fit a negative binomial assumption: genes with many zeros and individual very large counts are difficult to model with the negative binomial distribution.

Usage

plotSparsity(x, normalized = TRUE, ...)

Arguments

Examples

dds <- makeExampleDESeqDataSet(n=1000,m=4,dispMeanRel=function(x) .5)
dds <- estimateSizeFactors(dds)
plotSparsity(dds)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/plotSparsity.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotSparsity
> ### Title: Sparsity plot
> ### Aliases: plotSparsity
> 
> ### ** Examples
> 
> 
> dds <- makeExampleDESeqDataSet(n=1000,m=4,dispMeanRel=function(x) .5)
> dds <- estimateSizeFactors(dds)
> plotSparsity(dds)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>