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Last data update: 2014.03.03

R: Density plot of CuffData

csDensity

R Documentation

Density plot of CuffData

Description

Creates a smoothed density plot, by sample, for log10 FPKM values from a cuffdiff run.

Usage

## S4 method for signature 'CuffData'
csDensity(object, logMode=TRUE, pseudocount=0, labels, features=FALSE, replicates=FALSE,...)
## S4 method for signature 'CuffFeatureSet'
csDensity(object, logMode=TRUE, pseudocount=0, labels, features=FALSE, replicates=FALSE,...)

Arguments

`object`	An object of class CuffData.
`logMode`	A logical value of whether or not to log10-transform FPKM values. By default this is TRUE.
`pseudocount`	Pseudocount value added to FPKM to avoid errors in log-transformation of true zero values.
`labels`	A list of tracking_id values or gene_short_name values used for 'callout' points on the density plot for reference. (Not implemented yet).
`features`	Will include all fields from 'features' slot in returned ggplot object. Useful for further manipulations of plot object using feature-level attributes (e.g. gene_type, class_code, etc)
`replicates`	A logical value whether or not to plot individual replicates or aggregate condition values.
`...`	Additional arguments

Details

Creates a density plot, by sample, for log10-transformed FPKM values from a cuffdiff run.

Value

A ggplot2 plot object

Note

None

Author(s)

Loyal A. Goff

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<-csDensity(genes) #Create csDensity plot
	d #Render plot

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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/csDensity.Rd_%03d_medium.png", width=480, height=480)
> ### Name: csDensity
> ### Title: Density plot of CuffData
> ### Aliases: csDensity csDensity,CuffData-method
> ###   csDensity,CuffFeatureSet-method
> 
> ### ** Examples
> 
> 	a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Create CuffSet object from sample data
> 	genes<-a@genes #Create CuffData object for all 'genes'
> 	d<-csDensity(genes) #Create csDensity plot
> 	d #Render plot
Warning message:
Removed 204 rows containing non-finite values (stat_density). 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>