csScatter {cummeRbund} | 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

[Package cummeRbund version 2.34.0 Index]