# A treemap R script produced by the REVIGO server at http://revigo.irb.hr/
# If you found REVIGO useful in your work, please cite the following reference:
# Supek F et al. "REVIGO summarizes and visualizes long lists of Gene Ontology
# terms" PLoS ONE 2011. doi:10.1371/journal.pone.0021800

# author: Anton Kratz <anton.kratz@gmail.com>, RIKEN Omics Science Center, Functional Genomics Technology Team, Japan
# created: Fri, Nov 02, 2012  7:25:52 PM
# last change: Fri, Nov 09, 2012  3:20:01 PM

# -----------------------------------------------------------------------------
# If you don't have the treemap package installed, uncomment the following line:
# install.packages( "treemap" );
library(treemap) 								# treemap package by Martijn Tennekes

# Set the working directory if necessary
# setwd("C:/Users/username/workingdir");

# --------------------------------------------------------------------------
# Here is your data from REVIGO. Scroll down for plot configuration options.

revigo.names <- c("term_ID","description","freqInDbPercent","abslog10pvalue","uniqueness","dispensability","representative");
revigo.data <- rbind(c("GO:0006412","translation",4.967,23.1574,0.739,0.000,"translation"),
c("GO:0009142","nucleoside triphosphate biosynthetic process",0.924,1.7901,0.566,0.223,"translation"),
c("GO:0006414","translational elongation",0.665,4.8794,0.770,0.513,"translation"),
c("GO:0006457","protein folding",0.973,3.3197,0.806,0.538,"translation"),
c("GO:0043094","cellular metabolic compound salvage",0.248,1.3866,0.826,0.191,"translation"),
c("GO:0009853","photorespiration",0.026,1.7208,0.843,0.153,"translation"),
c("GO:0009415","response to water",0.029,1.7725,0.842,0.000,"response to water"),
c("GO:0009414","response to water deprivation",0.020,1.7208,0.843,0.658,"response to water"),
c("GO:0015992","proton transport",1.025,2.3149,0.852,0.000,"proton transport"),
c("GO:0015031","protein transport",1.777,2.0398,0.773,0.318,"proton transport"),
c("GO:0006818","hydrogen transport",1.025,2.3149,0.852,0.299,"proton transport"),
c("GO:0048316","seed development",0.020,1.5117,0.815,0.000,"seed development"),
c("GO:0007031","peroxisome organization",0.026,2.0567,0.908,0.022,"peroxisome organization"),
c("GO:0044275","cellular carbohydrate catabolic process",0.982,1.3154,0.858,0.080,"cellular carbohydrate catabolism"),
c("GO:0045333","cellular respiration",4.810,2.2245,0.759,0.081,"cellular respiration"),
c("GO:0006091","generation of precursor metabolites and energy",6.142,2.5946,0.854,0.085,"generation of precursor metabolites and energy"));

stuff <- data.frame(revigo.data);
names(stuff) <- revigo.names;

stuff$abslog10pvalue <- as.numeric( as.character(stuff$abslog10pvalue) );
stuff$freqInDbPercent <- as.numeric( as.character(stuff$freqInDbPercent) );
stuff$uniqueness <- as.numeric( as.character(stuff$uniqueness) );
stuff$dispensability <- as.numeric( as.character(stuff$dispensability) );

# by default, outputs to a PDF file
pdf( file="revigo_treemap.pdf", width=16, height=9 ) # width and height are in inches

# check the tmPlot command documentation for all possible parameters - there are a lot more
tmPlot(
	stuff,
	index = c("representative","description"),
	vSize = "abslog10pvalue",
	type = "categorical",
	vColor = "representative",
	title = "REVIGO Gene Ontology treemap",
	inflate.labels = FALSE,      # set this to TRUE for space-filling group labels - good for posters
	lowerbound.cex.labels = 0,   # try to draw as many labels as possible (still, some small squares may not get a label)
	bg.labels = "#CCCCCCAA",     # define background color of group labels
												       # "#CCCCCC00" is fully transparent, "#CCCCCCAA" is semi-transparent grey, NA is opaque
	position.legend = "none"
)

dev.off()