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" 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.