Arguments
x
either an object of class 'tTest', or a numeric vector of log ratios, i.e. the log of the fold change values;
the names of the logRatio vector will be used to display the names of the most
interesting genes
y
should not be given if an object of class 'tTest' is passed as argument 'x';
if 'x' is a numeric vector of log ratios, 'y' should be given and should be a
numeric vector of P-values indicating the statistical significance
pointLabels
Labels for points on the volcano plot that are interesting
taking into account both the x and y dimensions; typically this is a
vector of gene symbols; most methods can access the gene symbols directly from
the object passed as 'x' argument; the argument allows for custom labels if
needed
topPValues
top n points that will be included in the points to label based
on their low P Values
topLogRatios
top n points that will be included in the points to label based
on their high absolute values of the log ratio
smoothScatter
use color saturation to indicate dots that are in densely
populated regions of the graph; defaults to TRUE
xlab
label for the x axis (string)
ylab
label for the y axis (string)
main
main title for the graph (string)
sub
subtitle for the graph (string)