volcano {IntegratedJM} | R Documentation |
volcano
Description
The volcano function produces the volcano plot for logratio / fp-effect vs corresponding p-values.
Usage
volcano(x, pValue, pointLabels, topPValues = 10, topXvalues = 10,
smoothScatter = TRUE, xlab = NULL, ylab = NULL, main = NULL,
newpage = TRUE, additionalPointsToLabel = NULL,
additionalLabelColor = "red", dir = TRUE)
Arguments
x |
Numeric vector of logratios or covariate effect values to be plotted. |
pValue |
Numeric vector of corresponding p-values obtained from some statistical test. |
pointLabels |
Character vector providing the texts for the points to be labelled in the plot. |
topPValues |
Number of top p-values to be labelled. Default value is 10. |
topXvalues |
Number of top logratios or covariate effect values to be labelled. Default value is 10. |
smoothScatter |
Logical parameter to decide if a smooth plot is expected or not. Default is TRUE. |
xlab |
Text for the x-axis of the plot. Default is NULL. |
ylab |
Text for the y-axis of the plot. Default is NULL. |
main |
Text for the main title of the plot. Default is NULL. |
newpage |
Logical parameter |
additionalPointsToLabel |
Set of points other than the top values to be labelled in the plot. Default is NULL. |
additionalLabelColor |
Colour of the additionally labelled points. Default colour is red. |
dir |
Logical parameter deciding if the top values should be in decreasing (= TRUE) or increasing (= FALSE) order. Default is TRUE. |
Details
Creates a plot which looks like a volcano with the interesting points labelled within the plot.
Value
A plot which looks like a volcano.
Examples
## Not run:
volcano(x=jmRes$CovEffect1,pValue=jmRes$rawP1,pointLabels=rownames(jmRes),
topPValues = 10, topXvalues = 10,xlab="FP Effect (alpha)",ylab="-log(p-values)")
## End(Not run)