csScatter: Scatter Plot

In gofflab/cummeRbund-BioC-Bridge: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

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

gofflab/cummeRbund-BioC-Bridge documentation built on May 17, 2019, 7:30 a.m.