superFreq (version 1.2.3)

plotMA: a plotting function for MA plots.

Description

a plotting function for MA plots.

Usage

plotMA(x, y, col = mcri("darkblue"), libNorm = F, span = 0.2,
  medianSigma = T, xlab = "A = log2(x*y)/2", ylab = "M = log2(x/y)",
  loess = F, cex = 0.6, pch = 16, verbose = T, ...)

Arguments

x

The x coordinates. Large x will push points towards up right.

y

The y coordinates. Large y will push points towards up right.

col

The base colour of the dots.

libNorm

If library normalisation should be perform on x and y before plotting.

span

The span of the loess fit. Higher values gives smoother fits.

medianSigma

Boolean. Prints the median deviation from 0 compared to poisson standard deviation. This is a good measure of how much systematic differences there are between x and y.

loess

Boolean. Plots a loess fit of the data.

verbose

Boolean. Outputs some messages while plotting.

...

Remaining arguments are passed on to plot(...).

Details

This plotting function does normal MA plots, with nice density visuals. Also have a range of options for things such as library normalisation and loess fits.

Examples

# NOT RUN {
x = rpois(3000, 1:3000)
y = rpois(3000, 1:3000)
plotMA(x, y)
plotMA(x, y, loess=T)

x = rpois(3000, round((1:3000)*1.2))
y = rpois(3000, 1:3000)
plotMA(x, y, loess=T)

# }