comboplot_scatter_boxplot-methods: A combination plot: sorted scatter plot and boxplot

Description Usage Arguments Value input types Author(s) Examples

Description

A 2 panel plot of a sorted numeric vector (from low to high), and a boxplot on the right. Additionally, a percentiles axis is added to the top, and a grid is plotted if do.percentiles=TRUE. Useful for plotting gene expression data for determining a cutoff.

Usage

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  comboplot_scatter_boxplot(x, main, xlab, ylab,
    do.percentiles, do.layout, ylim, ...)

  comboplot_scatter_boxplot.ExpressionSet(x, main = "",
    xlab = "Index", ylab = "Expression level (log2)",
    do.percentiles = TRUE, do.layout = TRUE,
    ylim = range(exprs(x), na.rm = TRUE), ...)

Arguments

x

a numeric vector, or an ExpressionSet object

main

see plot. If is(x, "ExpressionSet"), then leave main="", and the featureName will be used for each plot.

xlab

see plot

ylab

see plot

do.percentiles

logical: if TRUE, then add a percentiles axis and grid to the plot

do.layout

logical: if TRUE, then layout the plotting region. Set to FALSE if you'd rather do this once, first in a large loop.

ylim

numeric(2) of the min and max on the y-axis.

...

arguments passed to plot

Value

nothing.

input types

x can be a numeric vector; x can be an ExpressionSet, with >=1 features/genes (1 plot will be made per feature).

Author(s)

Mark Cowley, 2012-09-12

Examples

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if( interactive() ) {
  dat <- rnorm(100)
  comboplot_scatter_boxplot(dat)
  comboplot_scatter_boxplot(dat, do.percentiles=FALSE)
}

drmjc/mjcgraphics documentation built on May 15, 2019, 2:40 p.m.