MAplot

Description

Creates an M vs A plot (Avg intensity vs log ratio) for a given pair of conditions across all fpkms

Usage

## S4 method for signature 'CuffData'
MAplot(object,x,y,logMode=T,pseudocount=1,smooth=FALSE,useCount=FALSE)

Arguments

Details

None

Value

Returns a ggplot MvsA plot object.

Note

None

Author(s)

Loyal A. Goff and Cole Trapnell

References

None.

Examples

	a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data
	genes<-a@genes #Create CuffData object for all 'genes'
	d<-MAplot(genes,'hESC','Fibroblasts') #Create csDensity plot
	d #Render plot

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(cummeRbund)
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

Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: 'fastcluster'

The following object is masked from 'package:stats':

    hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid

Attaching package: 'cummeRbund'

The following object is masked from 'package:GenomicRanges':

    promoters

The following object is masked from 'package:IRanges':

    promoters

The following object is masked from 'package:BiocGenerics':

    conditions

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cummeRbund/MAplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MAplot
> ### Title: MAplot
> ### Aliases: MAplot MAplot,CuffData-method
> ### Keywords: heatmap
> 
> ### ** Examples
> 
> 	a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data
Creating database /home/ddbj/local/lib64/R/library/cummeRbund/extdata/cuffData.db
Reading Run Info File /home/ddbj/local/lib64/R/library/cummeRbund/extdata/run.info
Writing runInfo Table
Reading Read Group Info  /home/ddbj/local/lib64/R/library/cummeRbund/extdata/read_groups.info
Writing replicates Table
Reading /home/ddbj/local/lib64/R/library/cummeRbund/extdata/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading /home/ddbj/local/lib64/R/library/cummeRbund/extdata/gene_exp.diff
Writing geneExpDiffData table
Reading /home/ddbj/local/lib64/R/library/cummeRbund/extdata/promoters.diff
Writing promoterDiffData table
Reading /home/ddbj/local/lib64/R/library/cummeRbund/extdata/genes.count_tracking
Reshaping geneCount table
Recasting
Writing geneCount table
Reading read group info in /home/ddbj/local/lib64/R/library/cummeRbund/extdata/genes.read_group_tracking
Writing geneReplicateData table
Reading /home/ddbj/local/lib64/R/library/cummeRbund/extdata/isoforms.fpkm_tracking
Checking samples table...
OK!
Writing isoforms table
Reshaping isoformData table
Recasting
Writing isoformData table
Reading /home/ddbj/local/lib64/R/library/cummeRbund/extdata/isoform_exp.diff
Writing isoformExpDiffData table
Reading /home/ddbj/local/lib64/R/library/cummeRbund/extdata/isoforms.count_tracking
Reshaping isoformCount table
Recasting
Writing isoformCount table
Reading read group info in /home/ddbj/local/lib64/R/library/cummeRbund/extdata/isoforms.read_group_tracking
Writing isoformReplicateData table
Reading /home/ddbj/local/lib64/R/library/cummeRbund/extdata/tss_groups.fpkm_tracking
Checking samples table...
OK!
Writing TSS table
Reshaping TSSData table
Recasting
Writing TSSData table
Reading /home/ddbj/local/lib64/R/library/cummeRbund/extdata/tss_group_exp.diff
Writing TSSExpDiffData table
Reading /home/ddbj/local/lib64/R/library/cummeRbund/extdata/splicing.diff
Writing splicingDiffData table
Reading /home/ddbj/local/lib64/R/library/cummeRbund/extdata/tss_groups.count_tracking
Reshaping TSSCount table
Recasting
Writing TSSCount table
Reading read group info in /home/ddbj/local/lib64/R/library/cummeRbund/extdata/tss_groups.read_group_tracking
Writing TSSReplicateData table
Reading /home/ddbj/local/lib64/R/library/cummeRbund/extdata/cds.fpkm_tracking
Checking samples table...
OK!
Writing CDS table
Reshaping CDSData table
Recasting
Writing CDSData table
Reading /home/ddbj/local/lib64/R/library/cummeRbund/extdata/cds_exp.diff
Writing CDSExpDiffData table
Reading /home/ddbj/local/lib64/R/library/cummeRbund/extdata/cds.diff
Writing CDSDiffData table
Reading /home/ddbj/local/lib64/R/library/cummeRbund/extdata/cds.count_tracking
Reshaping CDSCount table
Recasting
Writing CDSCount table
Reading read group info in /home/ddbj/local/lib64/R/library/cummeRbund/extdata/cds.read_group_tracking
Writing CDSReplicateData table
Indexing Tables...
Warning messages:
1: attributes are not identical across measure variables; they will be dropped 
2: attributes are not identical across measure variables; they will be dropped 
3: attributes are not identical across measure variables; they will be dropped 
4: attributes are not identical across measure variables; they will be dropped 
5: attributes are not identical across measure variables; they will be dropped 
6: attributes are not identical across measure variables; they will be dropped 
7: attributes are not identical across measure variables; they will be dropped 
8: attributes are not identical across measure variables; they will be dropped 
> 	genes<-a@genes #Create CuffData object for all 'genes'
> 	d<-MAplot(genes,'hESC','Fibroblasts') #Create csDensity plot
> 	d #Render plot
Warning message:
Removed 54 rows containing missing values (geom_point). 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>