Usage
volcanoplotter(logRatio, pValue, pointLabels, topPValues = 10, topLogRatios = 10, logTransformP = TRUE, smoothScatter = TRUE, xlab = NULL, ylab = NULL,
main = NULL, sub = NULL, newpage = TRUE, additionalPointsToLabel = NULL, additionalLabelColor = "red")
Arguments
logRatio
numeric vector of log ratios
pValue
numeric vector of P values
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
logTransformP
if TRUE (default) -log10(pValue) is used for the plot
instead of the raw P values
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)
newpage
should the graph be drawn to a new grid page? Defaults to
TRUE. This argument is useful for including several volcano plots
in one layout.
additionalPointsToLabel
Entrez IDs of genes of interest, that will be highlighted on the plot; the color of highlighting is determined
by the 'additionalLabelColor' argument.
additionalLabelColor
Color used to highlight the 'additionalPointsToLabel'; defaults to "red".