Plot Arguments

Share:

Description

Utility function for generating a plot of a SAM or an EBAM object in an html output.

Usage

1
2
3
  plotArguments(pos.stats = NULL, sig.col = 3, xlim = NULL, ylim = NULL,
        main = NULL, xlab = NULL, ylab = NULL, pty = "s", lab = c(10, 10, 7),
        pch = NULL, sig.cex = 1, stats.cex = 0.8, y.intersp = 1.3)

Arguments

pos.stats

an integer between 0 and 2 for a SAM plot, and between 0 and 4 for an EBAM plot. See help.sam(plot) or help.ebam(plot), respectively, for how pos.stats can be specified, and for its default.

sig.col

a specification of the color of the significant genes. If sig.col has length 1, all the points corresponding to significant genes are marked in the color specified by sig.col. Only for a SAM plot: If length(sig.col) == 2, the down-regulated genes, i.e. the genes with negative expression score d, are marked in the color specified by sig.col[1], and the up-regulated genes, i.e. the genes with positive d, are marked in the color specified by sig.col[2]. For a description of how colors are specified, see par.

xlim

a numeric vector of length 2 specifying the x limits (minimum and maximum) of the plot.

ylim

a numeric vector of length 2 specifying the y limits of the plot.

main

a character string naming the main title of the plot.

xlab

a character string naming the label of the x axis.

ylab

a character string naming the label of the y axis.

pty

a character specifying the type of plot region to be used. "s" (default for a SAM plot) generates a square plotting region, and "m" (default for an EBAM plot) the maximal plotting region.

lab

a numeric vector of length 3 specifying the approximate number of tickmarks on the x axis and on the y axis and the label size.

pch

either an integer specifying a symbol or a single character to be used as the default in plotting points. For a description of how pch can be specified, see par.

sig.cex

a numerical value giving the amount by which the symbols of the significant genes should be scaled relative to the default.

stats.cex

the size of the statistics printed in the plot relative to the default size. Only available for an EBAM plot.

y.intersp

a numeric value specifying the space between the rows in which the statistics are plotted. Only available for an EBAM plot.

Value

A list required by sam2html or ebam2html if addPlot = TRUE.

Author(s)

Holger Schwender, holger.schw@gmx.de

See Also

sam2html,ebam2html

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.