volcanoplotter {a4Base} | R Documentation |
Workhorse function for the different volcanoPlot methods. A volcano plot is a graph that allows to simultaneously assess the P values (statistical significance) and log ratios (biological difference) of differential expression for the given genes.
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" )
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 |
smoothScatter |
use color saturation to indicate dots that are in densely
populated regions of the graph; defaults to |
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
|
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" |
a volcanoplot is drawn to the current device
Tobias Verbeke