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

limma::plotMA, 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)
```

*caroline*version 0.9.2 Index]