R: Generate a Ratio Average [RAy] Plot.

raPlot {caroline} | R Documentation

## Generate a Ratio Average [RAy] Plot.

### Description

A plot which turns two vectors of count data into log scaled fold change ratio and average abundance. The plot derives from a Bland-Altman plot and is also very similar to an MA plot. The RA plot is unique, however, in it's creative inclusion of the vector-unique 'arms' which are artificially introduced into the plot by adding a <1 epsilon factor before the log function is applied. The name RAy comes from the fact that the aforementioned 'uniques' arms addition makes it strongly resemble a geometric ray. Many of the parameters to the function play off of this convenient anatomical analogy.

### Usage

    raPlot(a, b=NULL, uniques=5, normalize=FALSE,
            nr=0, alpha = 0.01, jitter=FALSE, jit.wgts=NULL,
            rex=1, flat=TRUE, tail=.5, arms=.5, spine=1, border=NULL, plot=TRUE,  ...)

### Arguments

`a` | a vector of counts for a. can also be a matrix with two columns 1 for a and 2 for b.
`b` | a vector of counts for b.
`uniques` | a boolean specifying whether or not to plot the library-unique genes (those with zero counts in one or the other library).
`normalize` | A boolean specifying whether or not to normalize the counts into proportions.
`nr` | a numeric value indicating the asymptotic normalization ratio line.
`alpha` | a statisical significance value.
`jitter` | whether or not or how much to jitter the a and b counts into surrounding, non-overlapping space.
`jit.wgts` | a weight vector used to spread the counts of a and b into surrounding, non-overlapping space.
`rex` | a numeric value specifying the radial expansion of the plot points.
`flat` | a boolean for the radial expansion of points as a function of both R and A axes.
`tail` | a numeric or boolean value indicating the line thickness of the two trailing curved significance lines of the RAy.
`arms` | a numeric or boolean value indicating the line thickness of the two leading straight separator lines of the RAy.
`spine` | a numeric or boolean value indicating the line thickness of the normalization line (whose y position is specified by mm).
`border` | a vector of strings used to color the borders of the points.
`plot` | whether or not to do the actual plot.
`...` | other parameters passed to plot.

### Value

a RAy plot

### See Also

plotMA, link[edgeR]maPlot

### Examples

    a <- rnbinom(n=10000, mu=5, size=2)
    b <- rnbinom(n=10000, mu=5, size=2)

    ## the alternative
    plot(a,b)
    ## the raPlot version
    raPlot(a, b)

    ## highlight the condition unique points in the same way as  edgeR's "maPlot"
    RA <- raPlot(a, b, pch='')
    cond.unique <- apply(cbind(a,b), 1, function(d) any(d==0))
    points(RA$A,RA$R, col=c('black','orange')[cond.unique+1])

    ## try playing with jittering over plotted points
    raPlot(a, b, jitter=.3)

[Package caroline version 0.7.6 Index]