Generate maplot after differential expression test

Description

Generate maplot after differential expression test based on ggplot2

Usage

MAplot(stats, ylim, padj = TRUE, pcuff = 0.1, lfccuff = 1, 
   linecol = "red3", xlab = "mean of normalized counts",
   ylab = expression(log[2] ~ fold ~ change), shape) 

Arguments

Details

Generate classic MAplot for DE analysis using ggplot2, where A and M are from slot baseMean and slot log2FoldChange of the test statistics aftering calling XBSeqTest. The ggplot2 package generally generate figures of better quality as well as give user better control of the plotting system compared with the base plotting system.

Value

MAplot of test statistics

Author(s)

Yuanhang Liu

References

H. I. Chen, Y. Liu, Y. Zou, Z. Lai, D. Sarkar, Y. Huang, et al., "Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads," BMC Genomics, vol. 16 Suppl 7, p. S14, Jun 11 2015.

See Also

XBSeqTest

Examples

   conditions <- c(rep('C1', 3), rep('C2', 3))
   data(ExampleData)
   Stats <- XBSeq(Observed, Background, conditions)
   MAplot(Stats)

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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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(XBSeq)
Loading required package: 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")'.

    Welcome to 'XBSeq'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/XBSeq/MAplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MAplot
> ### Title: Generate maplot after differential expression test
> ### Aliases: MAplot
> 
> ### ** Examples
> 
>    conditions <- c(rep('C1', 3), rep('C2', 3))
>    data(ExampleData)
>    Stats <- XBSeq(Observed, Background, conditions)
>    MAplot(Stats)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>