volcanopar: Parameters used for the function volcanoplot

In CenterForStatistics-UGent/unifiedWMWqPCR: Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data

Parameters used for the function volcanoplot

Description

The parameters described can all be used in the different volcanoplot methods.

Arguments

highlight	an integer, indicating how many of the top features should be highlighted. Defaults to 0.
names	an optional character vector giving the names of the genes to be highlighted. If not specified, the features are numbered from most significant to least significant. Default value is NULL.
xlab	see par. Defaults to "Fit"
ylab	see par. Defaults to "Significance"
pch	see par. Defaults to 16
cex	see par. Defaults to 0.35 as in the limma package.
transf.x	a function used to transpose the values on the X axis. Defaults to NULL, unless otherwise specified in the specific methods.
transf.y	a function used to transpose the values on the Y axis. Defaults to NULL, unless otherwise specified in the specific method.
add.ref	a charater value indicating if reference lines for x, y or both axes should be drawn. It takes the values "none", "x", "y" or "both". Default value is "none". If not specified but ref.x or ref.y is, then the reference line is drawn for the X and/or the Y axis.
ref.x	a numerical vector, indicating the value or values at which the reference line(s) should be drawn on the X axis. Defaults to NULL.
ref.y	a numerical value, indicating the value at which the reference line should be drawn on the Y axis. Defaults to NULL unless otherwise specified in the specific methods.
col.x	The color for the reference line on the X axis. The argument is passed to the col argument of lines, so check that help page for possible values. Defaults to "darkgrey"
col.y	see col.x, but for the Y axis. If col.x is specified and col.y is not, then the value of col.x is used for col.y.
lwd.x	The line width for the reference line on the X axis. The argument is passed to the lwd argument of lines, so check that help page for possible values. Defaults to 1.
lwd.y	see lwd.x, but for the Y axis. If lwd.y is not specified and lwd.x is, that value is used for lwd.y as well.
lty.x	The line type for the reference line on the X axis. The argument is passed to the lty argument of lines, so check that help page for possible values. Defaults to 1.
lty.y	see lty.x, but for the Y axis. If lty.y is not specified and lty.x is, that value is used for lty.y as well.

Details

The arguments highlight and names are chosen in such a way that the function can mimick the behaviour of the volcanoplot function in the package limma.

Note

These parameters belong to the internal function, eventually called by the different S4 methods. This internal function is not exported, and should not be called directly.

Examples

# see the help page of volcanoplot

CenterForStatistics-UGent/unifiedWMWqPCR documentation built on Oct. 28, 2024, 2:34 p.m.