plotMA: a plotting function for MA plots.

In ChristofferFlensburg/superFreq: Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.

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

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)

ChristofferFlensburg/superFreq documentation built on Nov. 15, 2023, 6:15 a.m.