volcanoPlot {RNAither} | R Documentation |
Makes a volcano plot of the data.
volcanoPlot(header, dataset, col4plotx, col4ploty, col4anno, plotTitle, sigLevel, showPlot)
header |
the header of a dataset file generated with generateDatasetFile |
dataset |
an R data frame generated with generateDatasetFile |
col4plotx |
a character vector specifying the name of the column containing the intensity values, usually SigIntensity |
col4ploty |
a character vector specifying the name of the dataset column containing the corresponding p-values |
col4anno |
a character string specifying the name of the dataset column to be used to define the replicate, e.g. "GeneName" or "Internal_GeneID" . |
plotTitle |
the plot title |
sigLevel |
the significance level for the p-value, indicating where a horizontal green line will be drawn |
showPlot |
0 or 1. 1 will open one or several plot windows in the R GUI, 0 will only save the plot(s) without opening windows |
Plots the intensity values against the negative decadic logarithm of the p-values. A green horizontal line is drawn at the specified significance level.
The plot is saved in a pdf and a png file named after the experiment name specified in the header concatenated with the plotTitle
.
The function returns the plot name.
data(exampleHeader, package="RNAither") data(pValVec1, package="RNAither") data(scoredDataset1, package="RNAither") ##for details on the generation of pValVec1 and scoredDataset1, see the example of the Ttest function linked above. scoredHits1 <- hitselectionPval(scoredDataset1, pValVec1, "SigIntensity", "pValue.ttest_l", 0.05, "GeneName", "pvalue_testfile1.txt") hitDataset1 <- scoredHits1[[1]] hitvector1 <- scoredHits1[[2]] volcano_name <- volcanoPlot(header, hitDataset1, "SigIntensity", "pValue.ttest_l", "GeneName", "Volcano Plot", 0.05, 1)