Nothing

```
##This function produces plots from the GSEA analysis, in parallel for
##two phenotypes for one gene set.
pairwiseGseaPlot <- function(gl1, gl2, geneSet, exponent = 1,
output = "png", filepath, filename, ...){
##check arguments
paraCheck("genelist", gl1)
paraCheck("genelist", gl2)
paraCheck("gs", geneSet)
paraCheck("exponent", exponent)
paraCheck("output", output)
paraCheck("filepath", filepath)
paraCheck("filename", filename)
##The other arguments will be tested by the gseaScores function
##Compute the score, running sum and positions
gseaPh1 <- gseaScores(geneList = gl1, geneSet = geneSet,
exponent = exponent, mode = "graph")
gseaPh2 <- gseaScores(geneList = gl2, geneSet = geneSet,
exponent = exponent, mode = "graph")
##open a file
if(output == "pdf")
pdf(file = file.path(filepath, paste("pairwiseGsea_plots",
filename, sep = "")), ...=...)
if(output == "png")
png(filename = file.path(filepath, paste("pairwiseGsea_plots",
filename, sep = "")), ...=...)
##set graphical parameters
par(pin = c(5, 1.5), mfrow = c(2, 2), lwd = 1, mai = c(0.2, 0.8, 0.5, 0.1))
##Plot the phenotypes along the geneList, and add a vertical line
##for each match between geneList and gene set. This is done using
##the 'positions' output of gseaScores, which stores a one for each
##match position and a zero otherwise
plot(x = seq(1, length(gl1)), type = "l", y = gl1, ylab = "Phenotypes",
xlab = NA, col = "magenta", lwd = 2, xaxt = "n", main = "Phenotype 1")
abline(v = which(gseaPh1$positions == 1))
abline(h = 0)
par(mai = c(0.2, 0.8, 0.5, 0.1))
plot(x = seq(1, length(gl2)), type = "l", y = gl2, ylab = "Phenotypes",
xlab = NA, col = "magenta", lwd = 2, xaxt = "n", main = "Phenotype 2")
abline(v = which(gseaPh2$positions == 1))
abline(h = 0)
##Plot the running score and add a vertical line at the position of
##the enrichment score (maximal absolute value of the running score)
par(mai = c(1, 0.8, 0.1, 0.1))
plot(x = c(1:length(gseaPh1$runningScore)), y = gseaPh1$runningScore,
type = "l", xlab = "Position in the ranked list of genes",
ylab = "Running enrichment score")
abline(h = 0)
abline(v = which(gseaPh1$runningScore == gseaPh1$enrichmentScore),
lty = 3, col = "magenta", lwd = 3)
par(mai = c(1, 0.8, 0.1, 0.1))
plot(x = c(1:length(gseaPh2$runningScore)), y = gseaPh2$runningScore,
type = "l", xlab = "Position in the ranked list of genes",
ylab = "Running enrichment score")
abline(h = 0)
abline(v = which(gseaPh2$runningScore == gseaPh2$enrichmentScore),
lty = 3, col = "magenta", lwd = 3)
dev.off()
}
```

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