# 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);


# --------------------------------------------------------------------------
# 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:0006800","oxygen and reactive oxygen species metabolic process", 0.154, 1.746, 0.482, 4.210,-2.0916,0.993,0.000),
c("GO:0007626","locomotory behavior", 0.020,-1.127,-1.177, 3.364,-1.6635,0.971,0.000),
c("GO:0008283","cell proliferation", 0.143, 0.688,-0.413, 4.213,-1.0233,0.993,0.000),
c("GO:0008380","RNA splicing", 0.170,-4.403, 0.095, 4.287,-10.7570,0.873,0.000),
c("GO:0016192","vesicle-mediated transport", 0.348, 0.752,-3.246, 4.598,-3.0506,0.963,0.000),
c("GO:0022610","biological adhesion", 0.544, 1.535, 0.454, 4.792,-2.2067,0.993,0.000),
c("GO:0055114","oxidation-reduction process",16.676, 1.515, 0.426, 6.279,-6.6635,0.982,0.013),
c("GO:0030716","oocyte fate determination", 0.001, 7.053, 3.378, 1.949,-2.6073,0.831,0.014),
c("GO:0035088","establishment or maintenance of apical/basal cell polarity", 0.002, 0.364,-0.151, 2.453,-1.3493,0.967,0.015),
c("GO:0007163","establishment or maintenance of cell polarity", 0.016, 1.278,-0.734, 3.262,-1.3900,0.971,0.016),
c("GO:0030029","actin filament-based process", 0.106, 0.223, 0.079, 4.084,-6.2848,0.968,0.019),
c("GO:0007010","cytoskeleton organization", 0.203, 4.652,-6.401, 4.363,-10.4486,0.734,0.020),
c("GO:0007017","microtubule-based process", 0.308, 0.515, 0.162, 4.546,-5.2226,0.965,0.021),
c("GO:0000910","cytokinesis", 0.236, 1.377,-0.792, 4.429,-1.2966,0.966,0.021),
c("GO:0045454","cell redox homeostasis", 0.541,-2.320,-6.580, 4.790,-4.6421,0.830,0.022),
c("GO:0007155","cell adhesion", 0.540, 0.899, 0.460, 4.789,-2.3218,0.949,0.024),
c("GO:0042743","hydrogen peroxide metabolic process", 0.046, 0.078, 0.233, 3.718,-1.8137,0.950,0.035),
c("GO:0017144","drug metabolic process", 0.079, 1.364,-0.408, 3.954,-1.4425,0.953,0.036),
c("GO:0015980","energy derivation by oxidation of organic compounds", 4.971, 0.035, 1.492, 5.753,-9.0182,0.887,0.052),
c("GO:0006518","peptide metabolic process", 0.211, 0.842,-0.635, 4.381,-1.4665,0.950,0.054),
c("GO:0006084","acetyl-CoA metabolic process", 0.531,-0.833, 1.696, 4.782,-6.2684,0.897,0.060),
c("GO:0006006","glucose metabolic process", 1.107,-2.471, 4.358, 5.101,-8.4908,0.805,0.065),
c("GO:0009820","alkaloid metabolic process", 0.004, 0.773,-0.343, 2.614,-2.7758,0.962,0.077),
c("GO:0051186","cofactor metabolic process", 3.543, 0.064,-0.033, 5.606,-3.3125,0.937,0.077),
c("GO:0006091","generation of precursor metabolites and energy", 6.142, 0.678, 0.017, 5.845,-18.0615,0.934,0.085),
c("GO:0043603","cellular amide metabolic process", 0.201,-0.516, 1.088, 4.361,-1.3966,0.926,0.108),
c("GO:0006890","retrograde vesicle-mediated transport, Golgi to ER", 0.005, 1.292,-3.698, 2.757,-1.6644,0.933,0.176),
c("GO:0048678","response to axon injury", 0.005,-1.164,-0.686, 2.717,-1.0101,0.968,0.214),
c("GO:0006090","pyruvate metabolic process", 0.041,-1.941, 3.892, 3.667,-4.3215,0.891,0.227),
c("GO:0006414","translational elongation", 0.665,-5.223,-0.203, 4.880,-6.7905,0.856,0.251),
c("GO:0051443","positive regulation of ubiquitin-protein ligase activity", 0.002,-4.750,-4.359, 2.332,-3.1308,0.797,0.259),
c("GO:0008104","protein localization", 1.847, 0.608,-3.219, 5.323,-2.8214,0.936,0.277),
c("GO:0001539","ciliary or flagellar motility", 0.387, 0.158,-2.295, 4.645,-2.3615,0.932,0.280),
c("GO:0010608","posttranscriptional regulation of gene expression", 0.218,-4.458,-5.493, 4.395,-2.4001,0.860,0.289),
c("GO:0006458","'de novo' protein folding", 0.014,-3.531, 0.488, 3.201,-1.7523,0.904,0.296),
c("GO:0015985","energy coupled proton transport, down electrochemical gradient", 0.663, 0.561,-2.967, 4.879,-2.4501,0.923,0.297),
c("GO:0016071","mRNA metabolic process", 0.719,-6.006, 1.462, 4.913,-7.6253,0.876,0.300),
c("GO:0018149","peptide cross-linking", 0.009,-4.099, 0.383, 3.019,-2.2912,0.901,0.306),
c("GO:0006818","hydrogen transport", 1.025, 0.862,-3.470, 5.067,-2.3529,0.961,0.312),
c("GO:0021682","nerve maturation", 0.000, 7.019, 3.712, 1.398,-1.6685,0.841,0.315),
c("GO:0007264","small GTPase mediated signal transduction", 0.496,-3.045,-6.036, 4.753,-2.5153,0.847,0.320),
c("GO:0010498","proteasomal protein catabolic process", 0.042,-5.246, 1.397, 3.680,-2.8750,0.847,0.321),
c("GO:0006558","L-phenylalanine metabolic process", 0.058,-2.169, 4.200, 3.818,-2.1048,0.874,0.323),
c("GO:0006471","protein ADP-ribosylation", 0.013,-3.674, 0.413, 3.180,-1.0960,0.899,0.339),
c("GO:0009894","regulation of catabolic process", 0.238,-3.470,-4.779, 4.433,-1.5155,0.836,0.345),
c("GO:0006108","malate metabolic process", 0.111,-1.993, 4.023, 4.103,-1.3029,0.885,0.346),
c("GO:0010035","response to inorganic substance", 0.247,-1.400,-1.171, 4.449,-2.4658,0.950,0.350),
c("GO:0007164","establishment of tissue polarity", 0.004, 6.839, 3.240, 2.685,-1.3497,0.853,0.359),
c("GO:0009205","purine ribonucleoside triphosphate metabolic process", 4.768,-3.629, 3.991, 5.735,-4.6946,0.775,0.369),
c("GO:0006749","glutathione metabolic process", 0.072,-2.315, 4.596, 3.915,-1.5837,0.878,0.372),
c("GO:0006769","nicotinamide metabolic process", 0.000,-1.681, 3.765, 0.954,-2.4131,0.874,0.373),
c("GO:0006396","RNA processing", 2.591,-5.102, 0.881, 5.470,-1.4256,0.857,0.395),
c("GO:0007566","embryo implantation", 0.003, 6.514, 3.525, 2.507,-1.6644,0.834,0.397),
c("GO:0051289","protein homotetramerization", 0.007, 4.827,-6.827, 2.888,-1.7869,0.804,0.403),
c("GO:0019991","septate junction assembly", 0.000, 4.667,-6.280, 1.690,-1.1969,0.816,0.413),
c("GO:0006457","protein folding", 0.973,-4.383, 0.388, 5.045,-5.6180,0.875,0.426),
c("GO:0044087","regulation of cellular component biogenesis", 0.077, 2.180,-7.863, 3.943,-3.2426,0.769,0.428),
c("GO:0043484","regulation of RNA splicing", 0.006,-4.388,-4.502, 2.846,-1.9392,0.824,0.443),
c("GO:0001700","embryonic development via the syncytial blastoderm", 0.003, 6.396, 3.268, 2.504,-1.0998,0.832,0.446),
c("GO:0030721","spectrosome organization", 0.000, 4.717,-6.623, 0.699,-1.6685,0.826,0.450),
c("GO:0051129","negative regulation of cellular component organization", 0.045, 2.169,-7.460, 3.711,-1.8220,0.737,0.458),
c("GO:0051340","regulation of ligase activity", 0.003,-2.657,-6.111, 2.598,-2.3526,0.892,0.470),
c("GO:0035152","regulation of tube architecture, open tracheal system", 0.001, 6.072,-0.142, 2.196,-2.7903,0.745,0.472),
c("GO:0008340","determination of adult lifespan", 0.009, 6.465, 3.300, 3.035,-1.6606,0.825,0.473),
c("GO:0006085","acetyl-CoA biosynthetic process", 0.004,-1.178, 1.683, 2.697,-2.2385,0.910,0.474),
c("GO:0045478","fusome organization", 0.000, 4.733,-6.518, 1.279,-1.6685,0.815,0.484),
c("GO:0051591","response to cAMP", 0.005,-1.268,-0.709, 2.749,-1.7936,0.959,0.490),
c("GO:0006213","pyrimidine nucleoside metabolic process", 0.201,-3.142, 4.340, 4.359,-1.4180,0.828,0.495),
c("GO:0043433","negative regulation of sequence-specific DNA binding transcription factor activity", 0.009,-4.328,-4.546, 2.999,-1.0960,0.817,0.499),
c("GO:0007276","gamete generation", 0.062, 5.984, 3.941, 3.846,-1.4704,0.848,0.500),
c("GO:0007444","imaginal disc development", 0.009, 6.504, 3.291, 2.991,-1.7166,0.816,0.504),
c("GO:0016044","cellular membrane organization", 0.166, 4.961,-7.029, 4.276,-1.6677,0.785,0.505),
c("GO:0060047","heart contraction", 0.013, 5.905, 3.763, 3.159,-1.1929,0.879,0.508),
c("GO:0019953","sexual reproduction", 0.086, 3.316, 2.030, 3.990,-1.0008,0.959,0.510),
c("GO:0051084","'de novo' posttranslational protein folding", 0.014,-3.649, 0.465, 3.194,-1.0462,0.904,0.516),
c("GO:0048754","branching morphogenesis of a tube", 0.021, 6.439, 3.260, 3.372,-1.3150,0.814,0.526),
c("GO:0010927","cellular component assembly involved in morphogenesis", 0.019, 7.363,-2.377, 3.332,-1.1170,0.660,0.527),
c("GO:0006413","translational initiation", 0.337,-5.140,-0.206, 4.584,-1.7656,0.863,0.533),
c("GO:0001763","morphogenesis of a branching structure", 0.026, 6.537, 3.308, 3.470,-1.3294,0.820,0.537),
c("GO:0006412","translation", 4.967,-5.425,-0.172, 5.753,-5.2041,0.832,0.538),
c("GO:0045429","positive regulation of nitric oxide biosynthetic process", 0.004,-2.747,-5.862, 2.619,-1.0462,0.842,0.541),
c("GO:0009992","cellular water homeostasis", 0.000,-1.493,-6.087, 1.623,-1.6685,0.886,0.541),
c("GO:0006112","energy reserve metabolic process", 0.129,-0.073, 1.299, 4.169,-1.8918,0.915,0.543),
c("GO:0007016","cytoskeletal anchoring at plasma membrane", 0.002, 2.098,-7.277, 2.401,-3.1273,0.682,0.560),
c("GO:0042692","muscle cell differentiation", 0.034, 6.845, 3.204, 3.589,-2.5846,0.785,0.563),
c("GO:0016052","carbohydrate catabolic process", 1.399,-2.748, 2.542, 5.203,-5.3516,0.867,0.564),
c("GO:0035317","imaginal disc-derived wing hair organization", 0.001, 7.717,-1.784, 2.004,-1.9392,0.666,0.567),
c("GO:0051235","maintenance of location", 0.032,-2.035,-6.842, 3.556,-1.9771,0.861,0.584),
c("GO:0005977","glycogen metabolic process", 0.128,-2.411, 1.716, 4.164,-1.8918,0.840,0.589),
c("GO:0043933","macromolecular complex subunit organization", 1.085, 4.793,-6.575, 5.092,-2.5019,0.781,0.593),
c("GO:0042775","mitochondrial ATP synthesis coupled electron transport", 0.315,-0.397, 1.030, 4.555,-2.1471,0.906,0.598),
c("GO:0044042","glucan metabolic process", 0.249,-2.581, 1.526, 4.452,-1.3150,0.900,0.600),
c("GO:0000302","response to reactive oxygen species", 0.096,-1.634,-0.999, 4.039,-2.2784,0.942,0.602),
c("GO:0009791","post-embryonic development", 0.098, 6.741, 3.432, 4.048,-1.0400,0.805,0.606),
c("GO:0051881","regulation of mitochondrial membrane potential", 0.003,-1.762,-6.343, 2.477,-1.1929,0.875,0.610),
c("GO:0051187","cofactor catabolic process", 0.531,-2.003, 1.740, 4.781,-5.0487,0.857,0.615),
c("GO:0006397","mRNA processing", 0.620,-4.812, 0.447, 4.849,-8.9747,0.856,0.621),
c("GO:0007265","Ras protein signal transduction", 0.221,-3.016,-5.950, 4.402,-2.4889,0.855,0.623),
c("GO:0010324","membrane invagination", 0.005, 4.527,-6.207, 2.777,-1.5812,0.822,0.623),
c("GO:0006122","mitochondrial electron transport, ubiquinol to cytochrome c", 0.011,-0.046, 1.282, 3.105,-1.6685,0.925,0.627),
c("GO:0016339","calcium-dependent cell-cell adhesion", 0.001, 1.454, 0.925, 2.201,-1.0433,0.961,0.632),
c("GO:0030030","cell projection organization", 0.278, 4.595,-6.258, 4.500,-2.1762,0.754,0.635),
c("GO:0006559","L-phenylalanine catabolic process", 0.019,-3.193, 4.142, 3.331,-2.2959,0.838,0.636),
c("GO:0006911","phagocytosis, engulfment", 0.005, 3.933,-6.093, 2.743,-1.0521,0.800,0.646),
c("GO:0006979","response to oxidative stress", 0.231,-1.328,-0.781, 4.420,-2.0583,0.950,0.646),
c("GO:0060537","muscle tissue development", 0.036, 7.109, 3.418, 3.618,-1.5332,0.829,0.653),
c("GO:0050684","regulation of mRNA processing", 0.005,-4.451,-4.710, 2.748,-1.7936,0.831,0.653),
c("GO:0008064","regulation of actin polymerization or depolymerization", 0.026, 2.277,-7.882, 3.464,-7.1506,0.637,0.655),
c("GO:0016358","dendrite development", 0.014, 7.757,-1.866, 3.188,-1.3150,0.635,0.658),
c("GO:0006897","endocytosis", 0.075, 1.104,-3.422, 3.934,-1.4100,0.960,0.660),
c("GO:0002165","instar larval or pupal development", 0.010, 6.788, 3.450, 3.036,-1.3715,0.823,0.662),
c("GO:0032268","regulation of cellular protein metabolic process", 0.389,-5.610,-4.601, 4.647,-2.1629,0.775,0.664),
c("GO:0030163","protein catabolic process", 0.408,-4.815, 1.164, 4.667,-1.3202,0.857,0.670),
c("GO:0010033","response to organic substance", 0.355,-1.432,-1.226, 4.607,-1.1732,0.949,0.670),
c("GO:0034220","ion transmembrane transport", 1.198, 0.079,-2.078, 5.135,-2.0607,0.923,0.670),
c("GO:0006570","tyrosine metabolic process", 0.045,-2.101, 4.168, 3.706,-1.3029,0.876,0.672),
c("GO:0042554","superoxide anion generation", 0.002, 1.264, 0.986, 2.350,-1.0462,0.957,0.675),
c("GO:0006119","oxidative phosphorylation", 0.910,-0.090, 1.331, 5.016,-4.2692,0.905,0.680),
c("GO:0019362","pyridine nucleotide metabolic process", 0.466,-3.544, 4.591, 4.725,-3.9281,0.786,0.682),
c("GO:0006631","fatty acid metabolic process", 0.734,-2.080, 4.102, 4.923,-1.1916,0.860,0.684),
c("GO:0007052","mitotic spindle organization", 0.006, 4.668,-6.421, 2.839,-4.1726,0.739,0.688),
c("GO:0060711","labyrinthine layer development", 0.005, 6.828, 3.510, 2.740,-1.0462,0.819,0.689),
c("GO:0009109","coenzyme catabolic process", 0.518,-2.402, 2.492, 4.771,-5.2684,0.849,0.689),
c("GO:0030865","cortical cytoskeleton organization", 0.007, 4.850,-6.747, 2.873,-1.7936,0.757,0.691),
c("GO:0009208","pyrimidine ribonucleoside triphosphate metabolic process", 0.044,-2.669, 4.173, 3.698,-1.0960,0.830,0.694),
c("GO:0032989","cellular component morphogenesis", 0.840, 7.493,-2.370, 4.981,-1.0284,0.622,0.695),
c("GO:0051100","negative regulation of binding", 0.024,-2.288,-5.303, 3.430,-1.0433,0.890,0.699));

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");