inst/extdata/GO/setE-4/treemap.R
In wikiselev/rnaseq.mcf10a: Supplementary R package to the paper "Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop"
# 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:0009887","organ morphogenesis",2.260,5.2076,0.596,0.000,"organ morphogenesis"),
c("GO:0007621","negative regulation of female receptivity",0.019,1.7445,0.781,0.253,"organ morphogenesis"),
c("GO:0045760","positive regulation of action potential",0.015,1.4475,0.940,0.279,"organ morphogenesis"),
c("GO:2000036","regulation of stem cell maintenance",0.040,2.7235,0.620,0.329,"organ morphogenesis"),
c("GO:0007468","regulation of rhodopsin gene expression",0.010,1.7445,0.672,0.339,"organ morphogenesis"),
c("GO:0048745","smooth muscle tissue development",0.058,2.7423,0.719,0.340,"organ morphogenesis"),
c("GO:0035262","gonad morphogenesis",0.001,1.7445,0.735,0.349,"organ morphogenesis"),
c("GO:0002930","trabecular meshwork development",0.007,1.7445,0.739,0.361,"organ morphogenesis"),
c("GO:0061144","alveolar secondary septum development",0.008,1.4475,0.697,0.365,"organ morphogenesis"),
c("GO:0033151","V(D)J recombination",0.049,1.7235,0.676,0.367,"organ morphogenesis"),
c("GO:0061549","sympathetic ganglion development",0.021,2.7235,0.691,0.381,"organ morphogenesis"),
c("GO:0061548","ganglion development",0.023,2.7235,0.691,0.384,"organ morphogenesis"),
c("GO:0048483","autonomic nervous system development",0.085,3.3188,0.702,0.385,"organ morphogenesis"),
c("GO:0072075","metanephric mesenchyme development",0.031,3.5229,0.626,0.407,"organ morphogenesis"),
c("GO:0007600","sensory perception",1.733,3.2840,0.738,0.409,"organ morphogenesis"),
c("GO:0035272","exocrine system development",0.178,1.4859,0.703,0.413,"organ morphogenesis"),
c("GO:0048863","stem cell differentiation",0.847,2.1331,0.661,0.415,"organ morphogenesis"),
c("GO:0060385","axonogenesis involved in innervation",0.017,4.2518,0.654,0.424,"organ morphogenesis"),
c("GO:0060666","dichotomous subdivision of terminal units involved in salivary gland branching",0.023,2.5072,0.657,0.434,"organ morphogenesis"),
c("GO:2001213","negative regulation of vasculogenesis",0.001,1.7445,0.664,0.436,"organ morphogenesis"),
c("GO:0021675","nerve development",0.234,2.3325,0.681,0.436,"organ morphogenesis"),
c("GO:0003008","system process",4.235,1.8156,0.728,0.462,"organ morphogenesis"),
c("GO:0045165","cell fate commitment",0.620,2.0630,0.669,0.471,"organ morphogenesis"),
c("GO:0097490","sympathetic neuron projection extension",0.017,2.7235,0.648,0.483,"organ morphogenesis"),
c("GO:0002062","chondrocyte differentiation",0.244,3.1135,0.601,0.492,"organ morphogenesis"),
c("GO:0003158","endothelium development",0.229,1.8811,0.688,0.502,"organ morphogenesis"),
c("GO:0072165","anterior mesonephric tubule development",0.001,1.7445,0.691,0.512,"organ morphogenesis"),
c("GO:0048546","digestive tract morphogenesis",0.149,1.7488,0.658,0.514,"organ morphogenesis"),
c("GO:0035265","organ growth",0.300,2.2668,0.764,0.518,"organ morphogenesis"),
c("GO:0009790","embryo development",2.628,2.6737,0.649,0.523,"organ morphogenesis"),
c("GO:0048712","negative regulation of astrocyte differentiation",0.030,2.3363,0.603,0.525,"organ morphogenesis"),
c("GO:0007413","axonal fasciculation",0.047,1.7975,0.658,0.533,"organ morphogenesis"),
c("GO:0060485","mesenchyme development",0.581,2.9914,0.626,0.544,"organ morphogenesis"),
c("GO:0030857","negative regulation of epithelial cell differentiation",0.059,2.5686,0.575,0.549,"organ morphogenesis"),
c("GO:0060437","lung growth",0.010,1.4475,0.708,0.551,"organ morphogenesis"),
c("GO:0072358","cardiovascular system development",2.258,2.1325,0.627,0.552,"organ morphogenesis"),
c("GO:0072359","circulatory system development",2.260,2.1325,0.638,0.552,"organ morphogenesis"),
c("GO:0007498","mesoderm development",0.291,2.1002,0.692,0.553,"organ morphogenesis"),
c("GO:0072513","positive regulation of secondary heart field cardioblast proliferation",0.007,1.7445,0.608,0.554,"organ morphogenesis"),
c("GO:0072148","epithelial cell fate commitment",0.039,1.9714,0.663,0.560,"organ morphogenesis"),
c("GO:0009888","tissue development",4.199,2.0991,0.675,0.561,"organ morphogenesis"),
c("GO:0072172","mesonephric tubule formation",0.007,3.4949,0.624,0.564,"organ morphogenesis"),
c("GO:0072194","kidney smooth muscle tissue development",0.007,1.4475,0.671,0.564,"organ morphogenesis"),
c("GO:0090185","negative regulation of kidney development",0.008,1.4475,0.631,0.569,"organ morphogenesis"),
c("GO:0048332","mesoderm morphogenesis",0.199,2.0035,0.644,0.570,"organ morphogenesis"),
c("GO:0042476","odontogenesis",0.418,2.4776,0.626,0.571,"organ morphogenesis"),
c("GO:0061227","pattern specification involved in mesonephros development",0.002,1.7445,0.698,0.574,"organ morphogenesis"),
c("GO:0043583","ear development",0.579,1.7064,0.653,0.575,"organ morphogenesis"),
c("GO:0035108","limb morphogenesis",0.455,1.4657,0.656,0.576,"organ morphogenesis"),
c("GO:0072166","posterior mesonephric tubule development",0.002,1.4475,0.681,0.582,"organ morphogenesis"),
c("GO:0048568","embryonic organ development",1.162,3.1135,0.621,0.586,"organ morphogenesis"),
c("GO:0002027","regulation of heart rate",0.190,1.4577,0.731,0.587,"organ morphogenesis"),
c("GO:0048793","pronephros development",0.014,1.4475,0.680,0.587,"organ morphogenesis"),
c("GO:0048732","gland development",1.335,2.9788,0.635,0.596,"organ morphogenesis"),
c("GO:0010470","regulation of gastrulation",0.060,1.5372,0.640,0.597,"organ morphogenesis"),
c("GO:0022008","neurogenesis",3.440,1.7053,0.556,0.607,"organ morphogenesis"),
c("GO:0072189","ureter development",0.034,2.0752,0.659,0.615,"organ morphogenesis"),
c("GO:0072184","renal vesicle progenitor cell differentiation",0.001,1.7445,0.663,0.617,"organ morphogenesis"),
c("GO:0060600","dichotomous subdivision of an epithelial terminal unit",0.033,1.9714,0.665,0.618,"organ morphogenesis"),
c("GO:0044707","single-multicellular organism process",15.092,2.4522,0.699,0.619,"organ morphogenesis"),
c("GO:0072259","metanephric interstitial fibroblast development",0.001,1.7445,0.675,0.624,"organ morphogenesis"),
c("GO:0045446","endothelial cell differentiation",0.201,2.0362,0.630,0.627,"organ morphogenesis"),
c("GO:0009653","anatomical structure morphogenesis",5.999,5.2291,0.664,0.639,"organ morphogenesis"),
c("GO:0072074","kidney mesenchyme development",0.040,3.2007,0.633,0.643,"organ morphogenesis"),
c("GO:0072111","cell proliferation involved in kidney development",0.047,1.8794,0.631,0.644,"organ morphogenesis"),
c("GO:0001958","endochondral ossification",0.074,1.4843,0.659,0.660,"organ morphogenesis"),
c("GO:0048729","tissue morphogenesis",1.464,1.9374,0.617,0.660,"organ morphogenesis"),
c("GO:0036075","replacement ossification",0.074,1.4843,0.799,0.661,"organ morphogenesis"),
c("GO:0042475","odontogenesis of dentin-containing tooth",0.342,1.7181,0.631,0.664,"organ morphogenesis"),
c("GO:0048638","regulation of developmental growth",0.309,2.3242,0.679,0.666,"organ morphogenesis"),
c("GO:0048869","cellular developmental process",8.570,2.5017,0.611,0.672,"organ morphogenesis"),
c("GO:0045596","negative regulation of cell differentiation",1.429,2.2557,0.557,0.683,"organ morphogenesis"),
c("GO:0048389","intermediate mesoderm development",0.002,1.4475,0.759,0.689,"organ morphogenesis"),
c("GO:2000027","regulation of organ morphogenesis",0.521,1.4657,0.576,0.690,"organ morphogenesis"),
c("GO:0021636","trigeminal nerve morphogenesis",0.016,1.7445,0.706,0.694,"organ morphogenesis"),
c("GO:0007605","sensory perception of sound",0.268,1.9751,0.772,0.696,"organ morphogenesis"),
c("GO:0009987","cellular process",59.614,1.7635,0.998,0.000,"cellular process"),
c("GO:0022610","biological adhesion",2.826,1.5025,0.995,0.000,"biological adhesion"),
c("GO:0023052","signaling",17.329,2.9318,0.996,0.000,"signaling"),
c("GO:0032501","multicellular organismal process",15.657,2.2741,0.996,0.000,"multicellular organismal process"),
c("GO:0032502","developmental process",13.055,2.1798,0.995,0.000,"developmental process"),
c("GO:0040011","locomotion",3.285,2.4711,0.995,0.000,"locomotion"),
c("GO:0043085","positive regulation of catalytic activity",3.352,1.8784,0.871,0.000,"positive regulation of catalytic activity"),
c("GO:0050789","regulation of biological process",49.744,2.7959,0.924,0.159,"positive regulation of catalytic activity"),
c("GO:2001033","negative regulation of double-strand break repair via nonhomologous end joining",0.001,1.7445,0.820,0.192,"positive regulation of catalytic activity"),
c("GO:0048519","negative regulation of biological process",8.588,2.8386,0.935,0.207,"positive regulation of catalytic activity"),
c("GO:0046022","positive regulation of transcription from RNA polymerase II promoter during mitosis",0.005,1.4475,0.859,0.212,"positive regulation of catalytic activity"),
c("GO:0090402","oncogene-induced cell senescence",0.002,1.4475,0.754,0.294,"positive regulation of catalytic activity"),
c("GO:0031049","programmed DNA elimination",0.001,1.7445,0.934,0.294,"positive regulation of catalytic activity"),
c("GO:0048583","regulation of response to stimulus",26.518,2.7122,0.912,0.322,"positive regulation of catalytic activity"),
c("GO:0050794","regulation of cellular process",28.971,2.9101,0.892,0.337,"positive regulation of catalytic activity"),
c("GO:0097045","phosphatidylserine exposure on blood platelet",0.001,1.7445,0.763,0.339,"positive regulation of catalytic activity"),
c("GO:0051387","negative regulation of neurotrophin TRK receptor signaling pathway",0.007,1.4475,0.777,0.343,"positive regulation of catalytic activity"),
c("GO:0032747","positive regulation of interleukin-23 production",0.007,1.4475,0.782,0.400,"positive regulation of catalytic activity"),
c("GO:0031662","positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle",0.001,1.7445,0.836,0.424,"positive regulation of catalytic activity"),
c("GO:0019220","regulation of phosphate metabolic process",4.763,1.5583,0.778,0.441,"positive regulation of catalytic activity"),
c("GO:1900122","positive regulation of receptor binding",0.005,1.7445,0.934,0.468,"positive regulation of catalytic activity"),
c("GO:0051174","regulation of phosphorus metabolic process",4.788,1.4989,0.801,0.512,"positive regulation of catalytic activity"),
c("GO:0031660","regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle",0.001,1.7445,0.852,0.544,"positive regulation of catalytic activity"),
c("GO:0043552","positive regulation of phosphatidylinositol 3-kinase activity",0.051,1.6560,0.808,0.571,"positive regulation of catalytic activity"),
c("GO:0045737","positive regulation of cyclin-dependent protein serine/threonine kinase activity",0.027,1.4843,0.803,0.632,"positive regulation of catalytic activity"),
c("GO:0051099","positive regulation of binding",0.197,1.5754,0.921,0.651,"positive regulation of catalytic activity"),
c("GO:1900747","negative regulation of vascular endothelial growth factor signaling pathway",0.009,1.4475,0.773,0.654,"positive regulation of catalytic activity"),
c("GO:0002543","activation of blood coagulation via clotting cascade",0.002,1.4475,0.763,0.690,"positive regulation of catalytic activity"),
c("GO:0050896","response to stimulus",47.248,1.9910,0.997,0.000,"response to stimulus"),
c("GO:0065007","biological regulation",51.216,2.1273,0.997,0.000,"biological regulation"),
c("GO:0071593","lymphocyte aggregation",0.003,1.7445,0.974,0.013,"lymphocyte aggregation"),
c("GO:0007155","cell adhesion",2.821,1.5085,0.992,0.500,"lymphocyte aggregation"),
c("GO:0010463","mesenchymal cell proliferation",0.222,4.7212,0.903,0.019,"mesenchymal cell proliferation"),
c("GO:0021869","forebrain ventricular zone progenitor cell division",0.013,1.4475,0.665,0.407,"mesenchymal cell proliferation"),
c("GO:0035988","chondrocyte proliferation",0.017,2.7235,0.930,0.415,"mesenchymal cell proliferation"),
c("GO:0070444","oligodendrocyte progenitor proliferation",0.010,1.4475,0.669,0.605,"mesenchymal cell proliferation"),
c("GO:0042127","regulation of cell proliferation",3.148,4.2007,0.799,0.642,"mesenchymal cell proliferation"),
c("GO:0050679","positive regulation of epithelial cell proliferation",0.313,2.7986,0.813,0.666,"mesenchymal cell proliferation"),
c("GO:2000729","positive regulation of mesenchymal cell proliferation involved in ureter development",0.007,1.4475,0.588,0.678,"mesenchymal cell proliferation"),
c("GO:0072089","stem cell proliferation",0.477,3.1135,0.913,0.697,"mesenchymal cell proliferation"),
c("GO:0007267","cell-cell signaling",2.522,3.7696,0.838,0.025,"cell-cell signaling"),
c("GO:0016477","cell migration",2.372,3.2441,0.846,0.117,"cell-cell signaling"),
c("GO:0006928","cellular component movement",3.830,2.5114,0.890,0.125,"cell-cell signaling"),
c("GO:0007154","cell communication",17.535,3.1938,0.869,0.173,"cell-cell signaling"),
c("GO:0033037","polysaccharide localization",0.002,1.7445,0.981,0.187,"cell-cell signaling"),
c("GO:0003131","mesodermal-endodermal cell signaling",0.001,1.7445,0.904,0.192,"cell-cell signaling"),
c("GO:1901660","calcium ion export",0.005,1.7445,0.959,0.196,"cell-cell signaling"),
c("GO:0006893","Golgi to plasma membrane transport",0.063,1.8274,0.954,0.243,"cell-cell signaling"),
c("GO:0046579","positive regulation of Ras protein signal transduction",0.098,3.5850,0.789,0.273,"cell-cell signaling"),
c("GO:0002768","immune response-regulating cell surface receptor signaling pathway",0.710,1.7812,0.787,0.336,"cell-cell signaling"),
c("GO:0030838","positive regulation of actin filament polymerization",0.178,1.4859,0.807,0.339,"cell-cell signaling"),
c("GO:0097369","sodium ion import",0.001,1.7445,0.925,0.348,"cell-cell signaling"),
c("GO:0007210","serotonin receptor signaling pathway",0.055,1.7445,0.830,0.353,"cell-cell signaling"),
c("GO:0051674","localization of cell",2.570,2.8996,0.972,0.365,"cell-cell signaling"),
c("GO:0071526","semaphorin-plexin signaling pathway",0.098,1.5372,0.824,0.371,"cell-cell signaling"),
c("GO:0007259","JAK-STAT cascade",0.253,1.9991,0.812,0.391,"cell-cell signaling"),
c("GO:0035986","senescence-associated heterochromatin focus assembly",0.003,1.4475,0.905,0.410,"cell-cell signaling"),
c("GO:0010646","regulation of cell communication",6.570,2.5317,0.784,0.448,"cell-cell signaling"),
c("GO:0016055","Wnt signaling pathway",0.887,1.4816,0.790,0.455,"cell-cell signaling"),
c("GO:0023057","negative regulation of signaling",2.197,2.8508,0.807,0.473,"cell-cell signaling"),
c("GO:0090080","positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway",0.013,3.4949,0.730,0.521,"cell-cell signaling"),
c("GO:0097491","sympathetic neuron projection guidance",0.017,2.7235,0.615,0.532,"cell-cell signaling"),
c("GO:0044700","single organism signaling",17.329,2.9318,0.865,0.533,"cell-cell signaling"),
c("GO:1902178","fibroblast growth factor receptor apoptotic signaling pathway",0.001,1.7445,0.825,0.550,"cell-cell signaling"),
c("GO:0071436","sodium ion export",0.010,1.4475,0.916,0.550,"cell-cell signaling"),
c("GO:0030111","regulation of Wnt signaling pathway",0.482,1.7011,0.784,0.556,"cell-cell signaling"),
c("GO:0007169","transmembrane receptor protein tyrosine kinase signaling pathway",1.599,2.3595,0.764,0.558,"cell-cell signaling"),
c("GO:0007167","enzyme linked receptor protein signaling pathway",2.356,1.6891,0.770,0.558,"cell-cell signaling"),
c("GO:1902285","semaphorin-plexin signaling pathway involved in neuron projection guidance",0.019,2.7235,0.571,0.579,"cell-cell signaling"),
c("GO:0010648","negative regulation of cell communication",2.203,2.8239,0.756,0.588,"cell-cell signaling"),
c("GO:0043066","negative regulation of apoptotic process",1.702,1.5390,0.793,0.594,"cell-cell signaling"),
c("GO:0035607","fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development",0.006,1.4475,0.616,0.597,"cell-cell signaling"),
c("GO:0048585","negative regulation of response to stimulus",2.501,2.5834,0.864,0.598,"cell-cell signaling"),
c("GO:0035459","cargo loading into vesicle",0.017,1.4475,0.932,0.600,"cell-cell signaling"),
c("GO:0060397","JAK-STAT cascade involved in growth hormone signaling pathway",0.032,2.5686,0.781,0.601,"cell-cell signaling"),
c("GO:0060416","response to growth hormone",0.079,1.8274,0.914,0.604,"cell-cell signaling"),
c("GO:0051057","positive regulation of small GTPase mediated signal transduction",0.113,3.4089,0.788,0.604,"cell-cell signaling"),
c("GO:0014911","positive regulation of smooth muscle cell migration",0.040,2.3363,0.822,0.617,"cell-cell signaling"),
c("GO:0023051","regulation of signaling",6.570,2.3036,0.850,0.648,"cell-cell signaling"),
c("GO:0051056","regulation of small GTPase mediated signal transduction",1.620,3.0132,0.760,0.649,"cell-cell signaling"),
c("GO:0007264","small GTPase mediated signal transduction",2.633,2.1561,0.769,0.650,"cell-cell signaling"),
c("GO:0009968","negative regulation of signal transduction",2.090,2.6364,0.728,0.667,"cell-cell signaling"),
c("GO:0046580","negative regulation of Ras protein signal transduction",0.081,1.8693,0.779,0.680,"cell-cell signaling"),
c("GO:0051058","negative regulation of small GTPase mediated signal transduction",0.082,1.8274,0.779,0.686,"cell-cell signaling"),
c("GO:0014812","muscle cell migration",0.136,1.7875,0.878,0.690,"cell-cell signaling"),
c("GO:0007166","cell surface receptor signaling pathway",8.919,2.6234,0.750,0.695,"cell-cell signaling"),
c("GO:0008283","cell proliferation",4.075,3.3872,0.962,0.027,"cell proliferation"),
c("GO:0035690","cellular response to drug",0.111,2.6091,0.869,0.040,"cellular response to drug"),
c("GO:0072720","response to dithiothreitol",0.001,1.7445,0.936,0.245,"cellular response to drug"),
c("GO:0036146","cellular response to mycotoxin",0.001,1.7445,0.900,0.303,"cellular response to drug"),
c("GO:0072721","cellular response to dithiothreitol",0.001,1.7445,0.895,0.303,"cellular response to drug"),
c("GO:0070848","response to growth factor",1.438,1.6216,0.904,0.404,"cellular response to drug"),
c("GO:0070887","cellular response to chemical stimulus",5.433,1.5227,0.827,0.624,"cellular response to drug"),
c("GO:0070141","response to UV-A",0.007,2.3363,0.965,0.048,"response to UV-A"),
c("GO:2000685","positive regulation of cellular response to X-ray",0.001,1.7445,0.876,0.444,"response to UV-A"),
c("GO:0007602","phototransduction",0.145,1.7698,0.801,0.619,"response to UV-A"),
c("GO:0006776","vitamin A metabolic process",0.011,3.0177,0.879,0.068,"vitamin A metabolism"),
c("GO:0015942","formate metabolic process",0.007,1.7445,0.881,0.185,"vitamin A metabolism"),
c("GO:0006184","GTP catabolic process",2.612,2.0958,0.760,0.272,"vitamin A metabolism"),
c("GO:0002149","hypochlorous acid biosynthetic process",0.002,1.7445,0.884,0.333,"vitamin A metabolism"),
c("GO:0019285","glycine betaine biosynthetic process from choline",0.002,1.4475,0.871,0.416,"vitamin A metabolism"),
c("GO:0009115","xanthine catabolic process",0.001,1.7445,0.870,0.419,"vitamin A metabolism"),
c("GO:0006524","alanine catabolic process",0.009,1.7445,0.841,0.462,"vitamin A metabolism"),
c("GO:0046513","ceramide biosynthetic process",0.089,1.9582,0.857,0.465,"vitamin A metabolism"),
c("GO:0002148","hypochlorous acid metabolic process",0.002,1.7445,0.888,0.518,"vitamin A metabolism"),
c("GO:0009078","pyruvate family amino acid metabolic process",0.009,1.7445,0.869,0.526,"vitamin A metabolism"),
c("GO:0009118","regulation of nucleoside metabolic process",1.901,1.9626,0.753,0.594,"vitamin A metabolism"),
c("GO:0019858","cytosine metabolic process",0.005,1.4475,0.877,0.612,"vitamin A metabolism"),
c("GO:1901068","guanosine-containing compound metabolic process",2.687,1.9566,0.803,0.628,"vitamin A metabolism"),
c("GO:0046110","xanthine metabolic process",0.002,1.4475,0.880,0.661,"vitamin A metabolism"),
c("GO:0006667","sphinganine metabolic process",0.005,1.4475,0.875,0.676,"vitamin A metabolism"),
c("GO:0051716","cellular response to stimulus",19.092,1.9880,0.911,0.093,"cellular response to stimulus"),
c("GO:0044763","single-organism cellular process",45.302,1.7844,0.908,0.171,"cellular response to stimulus"),
c("GO:0035978","histone H2A-S139 phosphorylation",0.001,1.7445,0.878,0.095,"histone H2A-S139 phosphorylation"),
c("GO:0032796","uropod organization",0.008,1.4475,0.898,0.176,"histone H2A-S139 phosphorylation"),
c("GO:0031119","tRNA pseudouridine synthesis",0.009,1.4475,0.925,0.198,"histone H2A-S139 phosphorylation"),
c("GO:0031052","chromosome breakage",0.001,1.7445,0.912,0.323,"histone H2A-S139 phosphorylation"),
c("GO:0070194","synaptonemal complex disassembly",0.001,1.7445,0.917,0.323,"histone H2A-S139 phosphorylation"),
c("GO:0018108","peptidyl-tyrosine phosphorylation",1.130,1.5056,0.883,0.456,"histone H2A-S139 phosphorylation"));
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()
wikiselev/rnaseq.mcf10a documentation built on May 4, 2019, 5:25 a.m.
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# 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:0009887","organ morphogenesis",2.260,5.2076,0.596,0.000,"organ morphogenesis"),
c("GO:0007621","negative regulation of female receptivity",0.019,1.7445,0.781,0.253,"organ morphogenesis"),
c("GO:0045760","positive regulation of action potential",0.015,1.4475,0.940,0.279,"organ morphogenesis"),
c("GO:2000036","regulation of stem cell maintenance",0.040,2.7235,0.620,0.329,"organ morphogenesis"),
c("GO:0007468","regulation of rhodopsin gene expression",0.010,1.7445,0.672,0.339,"organ morphogenesis"),
c("GO:0048745","smooth muscle tissue development",0.058,2.7423,0.719,0.340,"organ morphogenesis"),
c("GO:0035262","gonad morphogenesis",0.001,1.7445,0.735,0.349,"organ morphogenesis"),
c("GO:0002930","trabecular meshwork development",0.007,1.7445,0.739,0.361,"organ morphogenesis"),
c("GO:0061144","alveolar secondary septum development",0.008,1.4475,0.697,0.365,"organ morphogenesis"),
c("GO:0033151","V(D)J recombination",0.049,1.7235,0.676,0.367,"organ morphogenesis"),
c("GO:0061549","sympathetic ganglion development",0.021,2.7235,0.691,0.381,"organ morphogenesis"),
c("GO:0061548","ganglion development",0.023,2.7235,0.691,0.384,"organ morphogenesis"),
c("GO:0048483","autonomic nervous system development",0.085,3.3188,0.702,0.385,"organ morphogenesis"),
c("GO:0072075","metanephric mesenchyme development",0.031,3.5229,0.626,0.407,"organ morphogenesis"),
c("GO:0007600","sensory perception",1.733,3.2840,0.738,0.409,"organ morphogenesis"),
c("GO:0035272","exocrine system development",0.178,1.4859,0.703,0.413,"organ morphogenesis"),
c("GO:0048863","stem cell differentiation",0.847,2.1331,0.661,0.415,"organ morphogenesis"),
c("GO:0060385","axonogenesis involved in innervation",0.017,4.2518,0.654,0.424,"organ morphogenesis"),
c("GO:0060666","dichotomous subdivision of terminal units involved in salivary gland branching",0.023,2.5072,0.657,0.434,"organ morphogenesis"),
c("GO:2001213","negative regulation of vasculogenesis",0.001,1.7445,0.664,0.436,"organ morphogenesis"),
c("GO:0021675","nerve development",0.234,2.3325,0.681,0.436,"organ morphogenesis"),
c("GO:0003008","system process",4.235,1.8156,0.728,0.462,"organ morphogenesis"),
c("GO:0045165","cell fate commitment",0.620,2.0630,0.669,0.471,"organ morphogenesis"),
c("GO:0097490","sympathetic neuron projection extension",0.017,2.7235,0.648,0.483,"organ morphogenesis"),
c("GO:0002062","chondrocyte differentiation",0.244,3.1135,0.601,0.492,"organ morphogenesis"),
c("GO:0003158","endothelium development",0.229,1.8811,0.688,0.502,"organ morphogenesis"),
c("GO:0072165","anterior mesonephric tubule development",0.001,1.7445,0.691,0.512,"organ morphogenesis"),
c("GO:0048546","digestive tract morphogenesis",0.149,1.7488,0.658,0.514,"organ morphogenesis"),
c("GO:0035265","organ growth",0.300,2.2668,0.764,0.518,"organ morphogenesis"),
c("GO:0009790","embryo development",2.628,2.6737,0.649,0.523,"organ morphogenesis"),
c("GO:0048712","negative regulation of astrocyte differentiation",0.030,2.3363,0.603,0.525,"organ morphogenesis"),
c("GO:0007413","axonal fasciculation",0.047,1.7975,0.658,0.533,"organ morphogenesis"),
c("GO:0060485","mesenchyme development",0.581,2.9914,0.626,0.544,"organ morphogenesis"),
c("GO:0030857","negative regulation of epithelial cell differentiation",0.059,2.5686,0.575,0.549,"organ morphogenesis"),
c("GO:0060437","lung growth",0.010,1.4475,0.708,0.551,"organ morphogenesis"),
c("GO:0072358","cardiovascular system development",2.258,2.1325,0.627,0.552,"organ morphogenesis"),
c("GO:0072359","circulatory system development",2.260,2.1325,0.638,0.552,"organ morphogenesis"),
c("GO:0007498","mesoderm development",0.291,2.1002,0.692,0.553,"organ morphogenesis"),
c("GO:0072513","positive regulation of secondary heart field cardioblast proliferation",0.007,1.7445,0.608,0.554,"organ morphogenesis"),
c("GO:0072148","epithelial cell fate commitment",0.039,1.9714,0.663,0.560,"organ morphogenesis"),
c("GO:0009888","tissue development",4.199,2.0991,0.675,0.561,"organ morphogenesis"),
c("GO:0072172","mesonephric tubule formation",0.007,3.4949,0.624,0.564,"organ morphogenesis"),
c("GO:0072194","kidney smooth muscle tissue development",0.007,1.4475,0.671,0.564,"organ morphogenesis"),
c("GO:0090185","negative regulation of kidney development",0.008,1.4475,0.631,0.569,"organ morphogenesis"),
c("GO:0048332","mesoderm morphogenesis",0.199,2.0035,0.644,0.570,"organ morphogenesis"),
c("GO:0042476","odontogenesis",0.418,2.4776,0.626,0.571,"organ morphogenesis"),
c("GO:0061227","pattern specification involved in mesonephros development",0.002,1.7445,0.698,0.574,"organ morphogenesis"),
c("GO:0043583","ear development",0.579,1.7064,0.653,0.575,"organ morphogenesis"),
c("GO:0035108","limb morphogenesis",0.455,1.4657,0.656,0.576,"organ morphogenesis"),
c("GO:0072166","posterior mesonephric tubule development",0.002,1.4475,0.681,0.582,"organ morphogenesis"),
c("GO:0048568","embryonic organ development",1.162,3.1135,0.621,0.586,"organ morphogenesis"),
c("GO:0002027","regulation of heart rate",0.190,1.4577,0.731,0.587,"organ morphogenesis"),
c("GO:0048793","pronephros development",0.014,1.4475,0.680,0.587,"organ morphogenesis"),
c("GO:0048732","gland development",1.335,2.9788,0.635,0.596,"organ morphogenesis"),
c("GO:0010470","regulation of gastrulation",0.060,1.5372,0.640,0.597,"organ morphogenesis"),
c("GO:0022008","neurogenesis",3.440,1.7053,0.556,0.607,"organ morphogenesis"),
c("GO:0072189","ureter development",0.034,2.0752,0.659,0.615,"organ morphogenesis"),
c("GO:0072184","renal vesicle progenitor cell differentiation",0.001,1.7445,0.663,0.617,"organ morphogenesis"),
c("GO:0060600","dichotomous subdivision of an epithelial terminal unit",0.033,1.9714,0.665,0.618,"organ morphogenesis"),
c("GO:0044707","single-multicellular organism process",15.092,2.4522,0.699,0.619,"organ morphogenesis"),
c("GO:0072259","metanephric interstitial fibroblast development",0.001,1.7445,0.675,0.624,"organ morphogenesis"),
c("GO:0045446","endothelial cell differentiation",0.201,2.0362,0.630,0.627,"organ morphogenesis"),
c("GO:0009653","anatomical structure morphogenesis",5.999,5.2291,0.664,0.639,"organ morphogenesis"),
c("GO:0072074","kidney mesenchyme development",0.040,3.2007,0.633,0.643,"organ morphogenesis"),
c("GO:0072111","cell proliferation involved in kidney development",0.047,1.8794,0.631,0.644,"organ morphogenesis"),
c("GO:0001958","endochondral ossification",0.074,1.4843,0.659,0.660,"organ morphogenesis"),
c("GO:0048729","tissue morphogenesis",1.464,1.9374,0.617,0.660,"organ morphogenesis"),
c("GO:0036075","replacement ossification",0.074,1.4843,0.799,0.661,"organ morphogenesis"),
c("GO:0042475","odontogenesis of dentin-containing tooth",0.342,1.7181,0.631,0.664,"organ morphogenesis"),
c("GO:0048638","regulation of developmental growth",0.309,2.3242,0.679,0.666,"organ morphogenesis"),
c("GO:0048869","cellular developmental process",8.570,2.5017,0.611,0.672,"organ morphogenesis"),
c("GO:0045596","negative regulation of cell differentiation",1.429,2.2557,0.557,0.683,"organ morphogenesis"),
c("GO:0048389","intermediate mesoderm development",0.002,1.4475,0.759,0.689,"organ morphogenesis"),
c("GO:2000027","regulation of organ morphogenesis",0.521,1.4657,0.576,0.690,"organ morphogenesis"),
c("GO:0021636","trigeminal nerve morphogenesis",0.016,1.7445,0.706,0.694,"organ morphogenesis"),
c("GO:0007605","sensory perception of sound",0.268,1.9751,0.772,0.696,"organ morphogenesis"),
c("GO:0009987","cellular process",59.614,1.7635,0.998,0.000,"cellular process"),
c("GO:0022610","biological adhesion",2.826,1.5025,0.995,0.000,"biological adhesion"),
c("GO:0023052","signaling",17.329,2.9318,0.996,0.000,"signaling"),
c("GO:0032501","multicellular organismal process",15.657,2.2741,0.996,0.000,"multicellular organismal process"),
c("GO:0032502","developmental process",13.055,2.1798,0.995,0.000,"developmental process"),
c("GO:0040011","locomotion",3.285,2.4711,0.995,0.000,"locomotion"),
c("GO:0043085","positive regulation of catalytic activity",3.352,1.8784,0.871,0.000,"positive regulation of catalytic activity"),
c("GO:0050789","regulation of biological process",49.744,2.7959,0.924,0.159,"positive regulation of catalytic activity"),
c("GO:2001033","negative regulation of double-strand break repair via nonhomologous end joining",0.001,1.7445,0.820,0.192,"positive regulation of catalytic activity"),
c("GO:0048519","negative regulation of biological process",8.588,2.8386,0.935,0.207,"positive regulation of catalytic activity"),
c("GO:0046022","positive regulation of transcription from RNA polymerase II promoter during mitosis",0.005,1.4475,0.859,0.212,"positive regulation of catalytic activity"),
c("GO:0090402","oncogene-induced cell senescence",0.002,1.4475,0.754,0.294,"positive regulation of catalytic activity"),
c("GO:0031049","programmed DNA elimination",0.001,1.7445,0.934,0.294,"positive regulation of catalytic activity"),
c("GO:0048583","regulation of response to stimulus",26.518,2.7122,0.912,0.322,"positive regulation of catalytic activity"),
c("GO:0050794","regulation of cellular process",28.971,2.9101,0.892,0.337,"positive regulation of catalytic activity"),
c("GO:0097045","phosphatidylserine exposure on blood platelet",0.001,1.7445,0.763,0.339,"positive regulation of catalytic activity"),
c("GO:0051387","negative regulation of neurotrophin TRK receptor signaling pathway",0.007,1.4475,0.777,0.343,"positive regulation of catalytic activity"),
c("GO:0032747","positive regulation of interleukin-23 production",0.007,1.4475,0.782,0.400,"positive regulation of catalytic activity"),
c("GO:0031662","positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle",0.001,1.7445,0.836,0.424,"positive regulation of catalytic activity"),
c("GO:0019220","regulation of phosphate metabolic process",4.763,1.5583,0.778,0.441,"positive regulation of catalytic activity"),
c("GO:1900122","positive regulation of receptor binding",0.005,1.7445,0.934,0.468,"positive regulation of catalytic activity"),
c("GO:0051174","regulation of phosphorus metabolic process",4.788,1.4989,0.801,0.512,"positive regulation of catalytic activity"),
c("GO:0031660","regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle",0.001,1.7445,0.852,0.544,"positive regulation of catalytic activity"),
c("GO:0043552","positive regulation of phosphatidylinositol 3-kinase activity",0.051,1.6560,0.808,0.571,"positive regulation of catalytic activity"),
c("GO:0045737","positive regulation of cyclin-dependent protein serine/threonine kinase activity",0.027,1.4843,0.803,0.632,"positive regulation of catalytic activity"),
c("GO:0051099","positive regulation of binding",0.197,1.5754,0.921,0.651,"positive regulation of catalytic activity"),
c("GO:1900747","negative regulation of vascular endothelial growth factor signaling pathway",0.009,1.4475,0.773,0.654,"positive regulation of catalytic activity"),
c("GO:0002543","activation of blood coagulation via clotting cascade",0.002,1.4475,0.763,0.690,"positive regulation of catalytic activity"),
c("GO:0050896","response to stimulus",47.248,1.9910,0.997,0.000,"response to stimulus"),
c("GO:0065007","biological regulation",51.216,2.1273,0.997,0.000,"biological regulation"),
c("GO:0071593","lymphocyte aggregation",0.003,1.7445,0.974,0.013,"lymphocyte aggregation"),
c("GO:0007155","cell adhesion",2.821,1.5085,0.992,0.500,"lymphocyte aggregation"),
c("GO:0010463","mesenchymal cell proliferation",0.222,4.7212,0.903,0.019,"mesenchymal cell proliferation"),
c("GO:0021869","forebrain ventricular zone progenitor cell division",0.013,1.4475,0.665,0.407,"mesenchymal cell proliferation"),
c("GO:0035988","chondrocyte proliferation",0.017,2.7235,0.930,0.415,"mesenchymal cell proliferation"),
c("GO:0070444","oligodendrocyte progenitor proliferation",0.010,1.4475,0.669,0.605,"mesenchymal cell proliferation"),
c("GO:0042127","regulation of cell proliferation",3.148,4.2007,0.799,0.642,"mesenchymal cell proliferation"),
c("GO:0050679","positive regulation of epithelial cell proliferation",0.313,2.7986,0.813,0.666,"mesenchymal cell proliferation"),
c("GO:2000729","positive regulation of mesenchymal cell proliferation involved in ureter development",0.007,1.4475,0.588,0.678,"mesenchymal cell proliferation"),
c("GO:0072089","stem cell proliferation",0.477,3.1135,0.913,0.697,"mesenchymal cell proliferation"),
c("GO:0007267","cell-cell signaling",2.522,3.7696,0.838,0.025,"cell-cell signaling"),
c("GO:0016477","cell migration",2.372,3.2441,0.846,0.117,"cell-cell signaling"),
c("GO:0006928","cellular component movement",3.830,2.5114,0.890,0.125,"cell-cell signaling"),
c("GO:0007154","cell communication",17.535,3.1938,0.869,0.173,"cell-cell signaling"),
c("GO:0033037","polysaccharide localization",0.002,1.7445,0.981,0.187,"cell-cell signaling"),
c("GO:0003131","mesodermal-endodermal cell signaling",0.001,1.7445,0.904,0.192,"cell-cell signaling"),
c("GO:1901660","calcium ion export",0.005,1.7445,0.959,0.196,"cell-cell signaling"),
c("GO:0006893","Golgi to plasma membrane transport",0.063,1.8274,0.954,0.243,"cell-cell signaling"),
c("GO:0046579","positive regulation of Ras protein signal transduction",0.098,3.5850,0.789,0.273,"cell-cell signaling"),
c("GO:0002768","immune response-regulating cell surface receptor signaling pathway",0.710,1.7812,0.787,0.336,"cell-cell signaling"),
c("GO:0030838","positive regulation of actin filament polymerization",0.178,1.4859,0.807,0.339,"cell-cell signaling"),
c("GO:0097369","sodium ion import",0.001,1.7445,0.925,0.348,"cell-cell signaling"),
c("GO:0007210","serotonin receptor signaling pathway",0.055,1.7445,0.830,0.353,"cell-cell signaling"),
c("GO:0051674","localization of cell",2.570,2.8996,0.972,0.365,"cell-cell signaling"),
c("GO:0071526","semaphorin-plexin signaling pathway",0.098,1.5372,0.824,0.371,"cell-cell signaling"),
c("GO:0007259","JAK-STAT cascade",0.253,1.9991,0.812,0.391,"cell-cell signaling"),
c("GO:0035986","senescence-associated heterochromatin focus assembly",0.003,1.4475,0.905,0.410,"cell-cell signaling"),
c("GO:0010646","regulation of cell communication",6.570,2.5317,0.784,0.448,"cell-cell signaling"),
c("GO:0016055","Wnt signaling pathway",0.887,1.4816,0.790,0.455,"cell-cell signaling"),
c("GO:0023057","negative regulation of signaling",2.197,2.8508,0.807,0.473,"cell-cell signaling"),
c("GO:0090080","positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway",0.013,3.4949,0.730,0.521,"cell-cell signaling"),
c("GO:0097491","sympathetic neuron projection guidance",0.017,2.7235,0.615,0.532,"cell-cell signaling"),
c("GO:0044700","single organism signaling",17.329,2.9318,0.865,0.533,"cell-cell signaling"),
c("GO:1902178","fibroblast growth factor receptor apoptotic signaling pathway",0.001,1.7445,0.825,0.550,"cell-cell signaling"),
c("GO:0071436","sodium ion export",0.010,1.4475,0.916,0.550,"cell-cell signaling"),
c("GO:0030111","regulation of Wnt signaling pathway",0.482,1.7011,0.784,0.556,"cell-cell signaling"),
c("GO:0007169","transmembrane receptor protein tyrosine kinase signaling pathway",1.599,2.3595,0.764,0.558,"cell-cell signaling"),
c("GO:0007167","enzyme linked receptor protein signaling pathway",2.356,1.6891,0.770,0.558,"cell-cell signaling"),
c("GO:1902285","semaphorin-plexin signaling pathway involved in neuron projection guidance",0.019,2.7235,0.571,0.579,"cell-cell signaling"),
c("GO:0010648","negative regulation of cell communication",2.203,2.8239,0.756,0.588,"cell-cell signaling"),
c("GO:0043066","negative regulation of apoptotic process",1.702,1.5390,0.793,0.594,"cell-cell signaling"),
c("GO:0035607","fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development",0.006,1.4475,0.616,0.597,"cell-cell signaling"),
c("GO:0048585","negative regulation of response to stimulus",2.501,2.5834,0.864,0.598,"cell-cell signaling"),
c("GO:0035459","cargo loading into vesicle",0.017,1.4475,0.932,0.600,"cell-cell signaling"),
c("GO:0060397","JAK-STAT cascade involved in growth hormone signaling pathway",0.032,2.5686,0.781,0.601,"cell-cell signaling"),
c("GO:0060416","response to growth hormone",0.079,1.8274,0.914,0.604,"cell-cell signaling"),
c("GO:0051057","positive regulation of small GTPase mediated signal transduction",0.113,3.4089,0.788,0.604,"cell-cell signaling"),
c("GO:0014911","positive regulation of smooth muscle cell migration",0.040,2.3363,0.822,0.617,"cell-cell signaling"),
c("GO:0023051","regulation of signaling",6.570,2.3036,0.850,0.648,"cell-cell signaling"),
c("GO:0051056","regulation of small GTPase mediated signal transduction",1.620,3.0132,0.760,0.649,"cell-cell signaling"),
c("GO:0007264","small GTPase mediated signal transduction",2.633,2.1561,0.769,0.650,"cell-cell signaling"),
c("GO:0009968","negative regulation of signal transduction",2.090,2.6364,0.728,0.667,"cell-cell signaling"),
c("GO:0046580","negative regulation of Ras protein signal transduction",0.081,1.8693,0.779,0.680,"cell-cell signaling"),
c("GO:0051058","negative regulation of small GTPase mediated signal transduction",0.082,1.8274,0.779,0.686,"cell-cell signaling"),
c("GO:0014812","muscle cell migration",0.136,1.7875,0.878,0.690,"cell-cell signaling"),
c("GO:0007166","cell surface receptor signaling pathway",8.919,2.6234,0.750,0.695,"cell-cell signaling"),
c("GO:0008283","cell proliferation",4.075,3.3872,0.962,0.027,"cell proliferation"),
c("GO:0035690","cellular response to drug",0.111,2.6091,0.869,0.040,"cellular response to drug"),
c("GO:0072720","response to dithiothreitol",0.001,1.7445,0.936,0.245,"cellular response to drug"),
c("GO:0036146","cellular response to mycotoxin",0.001,1.7445,0.900,0.303,"cellular response to drug"),
c("GO:0072721","cellular response to dithiothreitol",0.001,1.7445,0.895,0.303,"cellular response to drug"),
c("GO:0070848","response to growth factor",1.438,1.6216,0.904,0.404,"cellular response to drug"),
c("GO:0070887","cellular response to chemical stimulus",5.433,1.5227,0.827,0.624,"cellular response to drug"),
c("GO:0070141","response to UV-A",0.007,2.3363,0.965,0.048,"response to UV-A"),
c("GO:2000685","positive regulation of cellular response to X-ray",0.001,1.7445,0.876,0.444,"response to UV-A"),
c("GO:0007602","phototransduction",0.145,1.7698,0.801,0.619,"response to UV-A"),
c("GO:0006776","vitamin A metabolic process",0.011,3.0177,0.879,0.068,"vitamin A metabolism"),
c("GO:0015942","formate metabolic process",0.007,1.7445,0.881,0.185,"vitamin A metabolism"),
c("GO:0006184","GTP catabolic process",2.612,2.0958,0.760,0.272,"vitamin A metabolism"),
c("GO:0002149","hypochlorous acid biosynthetic process",0.002,1.7445,0.884,0.333,"vitamin A metabolism"),
c("GO:0019285","glycine betaine biosynthetic process from choline",0.002,1.4475,0.871,0.416,"vitamin A metabolism"),
c("GO:0009115","xanthine catabolic process",0.001,1.7445,0.870,0.419,"vitamin A metabolism"),
c("GO:0006524","alanine catabolic process",0.009,1.7445,0.841,0.462,"vitamin A metabolism"),
c("GO:0046513","ceramide biosynthetic process",0.089,1.9582,0.857,0.465,"vitamin A metabolism"),
c("GO:0002148","hypochlorous acid metabolic process",0.002,1.7445,0.888,0.518,"vitamin A metabolism"),
c("GO:0009078","pyruvate family amino acid metabolic process",0.009,1.7445,0.869,0.526,"vitamin A metabolism"),
c("GO:0009118","regulation of nucleoside metabolic process",1.901,1.9626,0.753,0.594,"vitamin A metabolism"),
c("GO:0019858","cytosine metabolic process",0.005,1.4475,0.877,0.612,"vitamin A metabolism"),
c("GO:1901068","guanosine-containing compound metabolic process",2.687,1.9566,0.803,0.628,"vitamin A metabolism"),
c("GO:0046110","xanthine metabolic process",0.002,1.4475,0.880,0.661,"vitamin A metabolism"),
c("GO:0006667","sphinganine metabolic process",0.005,1.4475,0.875,0.676,"vitamin A metabolism"),
c("GO:0051716","cellular response to stimulus",19.092,1.9880,0.911,0.093,"cellular response to stimulus"),
c("GO:0044763","single-organism cellular process",45.302,1.7844,0.908,0.171,"cellular response to stimulus"),
c("GO:0035978","histone H2A-S139 phosphorylation",0.001,1.7445,0.878,0.095,"histone H2A-S139 phosphorylation"),
c("GO:0032796","uropod organization",0.008,1.4475,0.898,0.176,"histone H2A-S139 phosphorylation"),
c("GO:0031119","tRNA pseudouridine synthesis",0.009,1.4475,0.925,0.198,"histone H2A-S139 phosphorylation"),
c("GO:0031052","chromosome breakage",0.001,1.7445,0.912,0.323,"histone H2A-S139 phosphorylation"),
c("GO:0070194","synaptonemal complex disassembly",0.001,1.7445,0.917,0.323,"histone H2A-S139 phosphorylation"),
c("GO:0018108","peptidyl-tyrosine phosphorylation",1.130,1.5056,0.883,0.456,"histone H2A-S139 phosphorylation"));
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()
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