meanSdPlot {vsn} | R Documentation

## 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 `geom_hex`.
`...` | Further arguments that get passed on to `geom_hex`.

### 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 ...

[Package vsn version 3.62.0 Index]