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Last data update: 2014.03.03

R: Scatter Plot

csScatter

R Documentation

Scatter Plot

Description

A scatter plot comparing the FPKM values from two samples in a cuffdiff run.

Usage

## S4 method for signature 'CuffData'
csScatter(object, x, y, logMode=TRUE, pseudocount=1.0, labels, smooth=FALSE, colorByStatus = FALSE, drawRug=TRUE, ...)
## S4 method for signature 'CuffData'
csScatterMatrix(object,replicates=FALSE,logMode=TRUE,pseudocount=1.0, hexbin=FALSE, useCounts=FALSE, ...)

Arguments

`object`	An object of class ('CuffData','CuffFeatureSet')
`x`	Sample name for x axis
`y`	Sample name for y axis
`logMode`	Logical argument to render axes on log10 scale (default: T )
`replicates`	Logical argument whether or not to draw individual replicate values instead of condition values. (default: T )
`pseudocount`	Value to add to zero FPKM values for log transformation (default: 0.0001)
`smooth`	Logical argument to add a smooth-fit regression line
`labels`	A list of tracking_ids or gene_short_names that will be 'callout' points in the plot for reference. Useful for finding genes of interest in the field. Not implemented yet.
`colorByStatus`	A logical argument whether or not to color the points by 'significant' Y or N. [Default = FALSE]
`drawRug`	A logical argument whether or not to draw the rug for x and y axes [Default = TRUE]
`hexbin`	Logical value whether or not to visualize overplotting with hexbin.
`useCounts`	Uses normalized counts instead of FPKM.
`...`	Additional arguments to csScatter

Details

None

Value

ggplot object with geom_point and geom_rug layers

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
	s<-csScatter(genes,'hESC','Fibroblasts',smooth=TRUE) #Create plot object
	s #render plot object

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.
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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(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/csScatter.Rd_%03d_medium.png", width=480, height=480)
> ### Name: csScatter
> ### Title: Scatter Plot
> ### Aliases: csScatter csScatterMatrix csScatter,CuffData-method
> ###   csScatterMatrix,CuffData-method csScatter,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
> 	s<-csScatter(genes,'hESC','Fibroblasts',smooth=TRUE) #Create plot object
> 	s #render plot object
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>