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.

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]