vsn: meanSdPlot – R documentation

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meanSdPlot

Plot row standard deviations versus row means

Description

Methods for objects of classes matrix, ExpressionSet, vsn and MAList to plot row standard deviations versus row means.

Usage

meanSdPlot(x, 
           ranks = TRUE,
           xlab  = ifelse(ranks, "rank(mean)", "mean"),
           ylab  = "sd",
           pch,
           plot  = TRUE,
	   bins  = 50,
           ...)

Arguments

`x`	An object of class `matrix`, `ExpressionSet`, `vsn` or `MAList`.
`ranks`	Logical, indicating whether the x-axis (means) should be plotted on the original scale (`FALSE`) or on the rank scale (`TRUE`). The latter distributes the data more evenly along the x-axis and allows a better visual assessment of the standard deviation as a function of the mean.
`xlab`	Character, label for the x-axis.
`ylab`	Character, label for the y-axis.
`pch`	Ignored - exists for backward compatibility.
`plot`	Logical. If `TRUE` (default), a plot is produced. Calling the function with `plot=FALSE` can be useful if only its return value is of interest.
`bins`	Gets passed on to `stat_binhex`.
`...`	Further arguments that get passed on to `stat_binhex`.

Details

Standard deviation and mean are calculated row-wise from the expression matrix (in) x. The scatterplot of these versus each other allows you to visually verify whether there is a dependence of the standard deviation (or variance) on the mean. The red line depicts the running median estimator (window-width 10%). If there is no variance-mean dependence, then the line should be approximately horizontal.

Value

A named list with five components: its elements px and py are the x- and y-coordinates of the individual data points in the plot; its first and second element are the x-coordinates and values of the running median estimator (the red line in the plot). Its element gg is the plot object (see examples). Depending on the value of plot, the method can (and by default does) have a side effect, which is to print gg on the active graphics device.

Author(s)

Wolfgang Huber

Examples

data("kidney")
  log.na <- function(x) log(ifelse(x>0, x, NA))

  exprs(kidney) <- log.na(exprs(kidney))
  msd <- meanSdPlot(kidney)

  ## The `ggplot` object is returned in list element `gg`, here is an example of how to modify the plot
  library("ggplot2")
  msd$gg + ggtitle("Hello world") + scale_fill_gradient(low = "yellow", high = "darkred") + scale_y_continuous(limits = c(0, 7))  

  ## Try this out with not log-transformed data, vsn2-transformed data, the lymphoma data, your data ...

vsn

Variance stabilization and calibration for microarray data

v3.58.0

Artistic-2.0

Authors

Wolfgang Huber, with contributions from Anja von Heydebreck. Many comments and suggestions by users are acknowledged, among them Dennis Kostka, David Kreil, Hans-Ulrich Klein, Robert Gentleman, Deepayan Sarkar and Gordon Smyth

Initial release