pairwiseGseaPlot: Produce a plot for pairwise GSEA result on one gene set

Description

This function plots results of the GSEA analyses on one gene set for two phenotypes in parallel .

Usage

pairwiseGseaPlot(gl1, gl2, geneSet, exponent=1, output="png", filepath,
filename, ...)

Arguments

gl1

a named numeric or integer vector where names are gene identifiers of the same type as the ones in the gene set collection, and values are the measurements on phenotype one corresponding to those genes. This vector MUST be ordered

gl2

a named numeric or integer vector where names are gene identifiers of the same type as the ones in the gene set collection, and values are the measurements on phenotype two corresponding to those genes. This vector MUST be ordered

geneSet

a character vector specifying a gene set (no names, just a vector of characters corresponding to the IDs)

exponent

a single numeric or integer value (set as 1 by default) specifying the exponent of the GSEA method.

output

a single character value specifying the format of output figure: "pdf" or "png"

filepath

a single character value specifying the directory where these plots will be stored

filename

a single character value specifying the name of the gene set for which the plot is produced

...

other arguments of the function pdf or png

Details

The plots are going to be produced and stored in the directory 'filepath' with the name 'filename'.

References

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S. & Mesirov, J. P. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550.

Examples

Run this code

## Not run: 
# gl1 <- runif(100, min=-5, max=5)
# gl1 <- gl1[order(gl1, decreasing=TRUE)]
# gl2 <- runif(100, min=-5, max=5)
# gl2 <- gl2[order(gl2, decreasing=TRUE)]
# names(gl1) <- as.character(sample(x=seq(from=1, to=100, by=1), size=100,
# replace=FALSE))
# names(gl2) <- names(gl1)
# gs1 <- sample(names(gl1), size=20, replace=FALSE)
# gs2 <- sample(names(gl1), size=20, replace=FALSE)
# gsc <- list(subset1=gs1, subset2=gs2)
# pairwiseGseaPlot(gl1=gl1, gl2=gl2, geneSet=gsc[["subset1"]], filepath=".",
# filename="geneSet.pdf", output="pdf", width=8, height=6)
# ## End(Not run)