Expression Plot

Description

A line plot (optionally with confidence intervals) detailing FPKM expression levels across conditions for a given gene(s) or feature(s)

Usage

## S4 method for signature 'CuffFeature'
expressionPlot(object, logMode=FALSE, pseudocount=1.0, drawSummary=FALSE, sumFun=mean_cl_boot, showErrorbars=TRUE, showStatus=TRUE, replicates=FALSE, facet = TRUE,...)

Arguments

Details

None

Value

A ggplot2 plot object

Note

None

Author(s)

Loyal A. Goff

References

None

Examples

	data(sampleData)
	PINK1 # sample CuffFeature object
	expressionPlot(PINK1) #Line plot of PINK1 FPKM values
	expressionPlot(PINK1@isoforms) #Line plot of PINK1 FPKM values faceted by isoforms

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/expressionPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: expressionPlot
> ### Title: Expression Plot
> ### Aliases: expressionPlot expressionPlot,CuffFeature-method
> ###   expressionPlot,CuffFeatureSet-method
> 
> ### ** Examples
> 
> 	data(sampleData)
> 	PINK1 # sample CuffFeature object
CuffGene instance for gene XLOC_000172 
Short name:	 PINK1 
Slots:
	 annotation
	 features
	 fpkm
	 repFpkm
	 diff
	 count
	 isoforms	 CuffFeature instance of size 2 
	 TSS		 CuffFeature instance of size 2 
	 CDS		 CuffFeature instance of size 2 
> 	expressionPlot(PINK1) #Line plot of PINK1 FPKM values
> 	expressionPlot(PINK1@isoforms) #Line plot of PINK1 FPKM values faceted by isoforms
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>