cummeRbund (version 2.14.0)

csScatter: Scatter Plot

Description

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

Usage

"csScatter"(object, x, y, logMode=TRUE, pseudocount=1.0, labels, smooth=FALSE, colorByStatus = FALSE, drawRug=TRUE, ...)
"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

Value

ggplot object with geom_point and geom_rug layers

Details

None

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