# A plotting 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


# --------------------------------------------------------------------------
# If you don't have the ggplot2 package installed, uncomment the following line:
# install.packages( "ggplot2" );
library( ggplot2 );
# --------------------------------------------------------------------------
# If you don't have the scales package installed, uncomment the following line:
# install.packages( "scales" );
library( scales );


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

revigo.names <- c("term_ID","description","frequency_%","plot_X","plot_Y","plot_size","log10_p_value","uniqueness","dispensability");
revigo.data <- rbind(c("GO:0005230","extracellular ligand-gated ion channel activity", 0.057, 3.861, 5.472, 4.050,-2.9863,0.257,0.000),
c("GO:0005509","calcium ion binding", 0.554,-4.246, 5.747, 5.038,-1.3305,0.749,0.000),
c("GO:0030594","neurotransmitter receptor activity", 0.027, 4.444,-2.771, 3.723,-1.0890,0.852,0.000),
c("GO:0042165","neurotransmitter binding", 0.001,-0.505,-5.685, 2.288,-1.0538,0.831,0.030),
c("GO:0043167","ion binding",33.108,-5.724,-1.846, 6.815,-1.3528,0.833,0.081),
c("GO:0043169","cation binding",16.169,-5.411, 2.167, 6.503,-1.4025,0.760,0.211),
c("GO:0022803","passive transmembrane transporter activity", 0.517, 4.540, 4.077, 5.008,-1.5471,0.510,0.353),
c("GO:0046872","metal ion binding",15.851,-4.903, 3.571, 6.495,-1.4930,0.730,0.434));

one.data <- data.frame(revigo.data);
names(one.data) <- revigo.names;
one.data <- one.data [(one.data$plot_X != "null" & one.data$plot_Y != "null"), ];
one.data$plot_X <- as.numeric( as.character(one.data$plot_X) );
one.data$plot_Y <- as.numeric( as.character(one.data$plot_Y) );
one.data$plot_size <- as.numeric( as.character(one.data$plot_size) );
one.data$log10_p_value <- as.numeric( as.character(one.data$log10_p_value) );
one.data$frequency <- as.numeric( as.character(one.data$frequency) );
one.data$uniqueness <- as.numeric( as.character(one.data$uniqueness) );
one.data$dispensability <- as.numeric( as.character(one.data$dispensability) );
#head(one.data);


# --------------------------------------------------------------------------
# Names of the axes, sizes of the numbers and letters, names of the columns,
# etc. can be changed below

p1 <- ggplot( data = one.data );
p1 <- p1 + geom_point( aes( plot_X, plot_Y, colour = log10_p_value, size = plot_size), alpha = I(0.6) ) + scale_area();
p1 <- p1 + scale_colour_gradientn( colours = c("blue", "green", "yellow", "red"), limits = c( min(one.data$log10_p_value), 0) );
p1 <- p1 + geom_point( aes(plot_X, plot_Y, size = plot_size), shape = 21, fill = "transparent", colour = I (alpha ("black", 0.6) )) + scale_area();
p1 <- p1 + scale_size( range=c(5, 30)) + theme_bw(); # + scale_fill_gradientn(colours = heat_hcl(7), limits = c(-300, 0) );
ex <- one.data [ one.data$dispensability < 0.15, ]; 
p1 <- p1 + geom_text( data = ex, aes(plot_X, plot_Y, label = description), colour = I(alpha("black", 0.85)), size = 3 );
p1 <- p1 + labs (y = "semantic space x", x = "semantic space y");
p1 <- p1 + opts(legend.key = theme_blank()) ;
one.x_range = max(one.data$plot_X) - min(one.data$plot_X);
one.y_range = max(one.data$plot_Y) - min(one.data$plot_Y);
p1 <- p1 + xlim(min(one.data$plot_X)-one.x_range/10,max(one.data$plot_X)+one.x_range/10);
p1 <- p1 + ylim(min(one.data$plot_Y)-one.y_range/10,max(one.data$plot_Y)+one.y_range/10);



# --------------------------------------------------------------------------
# Output the plot to screen

p1;

# Uncomment the line below to also save the plot to a file.
# The file type depends on the extension (default=pdf).

# ggsave("C:/Users/path_to_your_file/revigo-plot.pdf");