inst/extdata/GO/setE-3/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:0016340","calcium-dependent cell-matrix adhesion",0.010,1.7040,0.995,0.000,"calcium-dependent cell-matrix adhesion"),
c("GO:0050896","response to stimulus",47.248,1.5715,0.997,0.000,"response to stimulus"),
c("GO:1901615","organic hydroxy compound metabolic process",1.118,4.0809,0.939,0.000,"organic hydroxy compound metabolism"),
c("GO:0006066","alcohol metabolic process",0.738,3.4949,0.845,0.103,"organic hydroxy compound metabolism"),
c("GO:0008209","androgen metabolic process",0.074,3.2518,0.726,0.161,"organic hydroxy compound metabolism"),
c("GO:0006629","lipid metabolic process",3.159,2.5302,0.881,0.234,"organic hydroxy compound metabolism"),
c("GO:0046655","folic acid metabolic process",0.019,2.1163,0.842,0.257,"organic hydroxy compound metabolism"),
c("GO:0006766","vitamin metabolic process",0.209,1.5412,0.892,0.312,"organic hydroxy compound metabolism"),
c("GO:0019048","modulation by virus of host morphology or physiology",0.033,2.2343,0.842,0.318,"organic hydroxy compound metabolism"),
c("GO:0050821","protein stabilization",0.131,3.0223,0.798,0.350,"organic hydroxy compound metabolism"),
c("GO:0002118","aggressive behavior",0.023,1.4073,0.961,0.363,"organic hydroxy compound metabolism"),
c("GO:0046340","diacylglycerol catabolic process",0.006,1.4073,0.816,0.394,"organic hydroxy compound metabolism"),
c("GO:0046490","isopentenyl diphosphate metabolic process",0.006,1.7040,0.820,0.394,"organic hydroxy compound metabolism"),
c("GO:0070143","mitochondrial alanyl-tRNA aminoacylation",0.001,1.7040,0.811,0.410,"organic hydroxy compound metabolism"),
c("GO:0032844","regulation of homeostatic process",0.737,2.4365,0.844,0.419,"organic hydroxy compound metabolism"),
c("GO:1901860","positive regulation of mitochondrial DNA metabolic process",0.002,1.4073,0.806,0.453,"organic hydroxy compound metabolism"),
c("GO:2000505","regulation of energy homeostasis",0.019,2.2573,0.780,0.493,"organic hydroxy compound metabolism"),
c("GO:0010960","magnesium ion homeostasis",0.025,1.4073,0.872,0.503,"organic hydroxy compound metabolism"),
c("GO:0010817","regulation of hormone levels",1.029,1.5748,0.856,0.510,"organic hydroxy compound metabolism"),
c("GO:1901194","negative regulation of formation of translation preinitiation complex",0.001,1.7040,0.793,0.526,"organic hydroxy compound metabolism"),
c("GO:0036112","medium-chain fatty-acyl-CoA metabolic process",0.003,1.7040,0.910,0.534,"organic hydroxy compound metabolism"),
c("GO:0032787","monocarboxylic acid metabolic process",1.329,1.6310,0.824,0.535,"organic hydroxy compound metabolism"),
c("GO:2000189","positive regulation of cholesterol homeostasis",0.007,1.4073,0.865,0.537,"organic hydroxy compound metabolism"),
c("GO:2000754","regulation of sphingomyelin catabolic process",0.001,1.7040,0.745,0.546,"organic hydroxy compound metabolism"),
c("GO:0019264","glycine biosynthetic process from serine",0.014,1.4073,0.829,0.561,"organic hydroxy compound metabolism"),
c("GO:0006419","alanyl-tRNA aminoacylation",0.009,1.4073,0.839,0.569,"organic hydroxy compound metabolism"),
c("GO:0031945","positive regulation of glucocorticoid metabolic process",0.001,1.7040,0.731,0.579,"organic hydroxy compound metabolism"),
c("GO:0001678","cellular glucose homeostasis",0.235,2.3487,0.814,0.606,"organic hydroxy compound metabolism"),
c("GO:0044255","cellular lipid metabolic process",2.183,2.8297,0.768,0.607,"organic hydroxy compound metabolism"),
c("GO:0051454","intracellular pH elevation",0.048,1.7040,0.831,0.626,"organic hydroxy compound metabolism"),
c("GO:0055067","monovalent inorganic cation homeostasis",0.235,1.8983,0.853,0.628,"organic hydroxy compound metabolism"),
c("GO:1901193","regulation of formation of translation preinitiation complex",0.001,1.7040,0.805,0.644,"organic hydroxy compound metabolism"),
c("GO:0016101","diterpenoid metabolic process",0.146,1.8661,0.790,0.646,"organic hydroxy compound metabolism"),
c("GO:0019395","fatty acid oxidation",0.155,1.5621,0.768,0.650,"organic hydroxy compound metabolism"),
c("GO:0001659","temperature homeostasis",0.074,2.0516,0.781,0.654,"organic hydroxy compound metabolism"),
c("GO:2000753","positive regulation of glucosylceramide catabolic process",0.001,1.7040,0.754,0.663,"organic hydroxy compound metabolism"),
c("GO:0033500","carbohydrate homeostasis",0.473,1.8681,0.847,0.667,"organic hydroxy compound metabolism"),
c("GO:2000225","negative regulation of testosterone biosynthetic process",0.001,1.7040,0.692,0.669,"organic hydroxy compound metabolism"),
c("GO:0046889","positive regulation of lipid biosynthetic process",0.108,1.6426,0.727,0.673,"organic hydroxy compound metabolism"),
c("GO:0006720","isoprenoid metabolic process",0.232,1.9618,0.795,0.677,"organic hydroxy compound metabolism"),
c("GO:0097009","energy homeostasis",0.046,1.7210,0.788,0.692,"organic hydroxy compound metabolism"),
c("GO:0044242","cellular lipid catabolic process",0.310,1.6983,0.775,0.697,"organic hydroxy compound metabolism"),
c("GO:1901863","positive regulation of muscle tissue development",0.039,3.0862,0.831,0.000,"positive regulation of muscle tissue development"),
c("GO:0045913","positive regulation of carbohydrate metabolic process",0.112,2.3645,0.826,0.121,"positive regulation of muscle tissue development"),
c("GO:0007379","segment specification",0.027,2.9508,0.856,0.220,"positive regulation of muscle tissue development"),
c("GO:0035265","organ growth",0.300,2.8327,0.870,0.229,"positive regulation of muscle tissue development"),
c("GO:0022038","corpus callosum development",0.025,1.8938,0.853,0.237,"positive regulation of muscle tissue development"),
c("GO:0042326","negative regulation of phosphorylation",0.763,1.8471,0.781,0.244,"positive regulation of muscle tissue development"),
c("GO:0045778","positive regulation of ossification",0.085,1.6807,0.821,0.249,"positive regulation of muscle tissue development"),
c("GO:0050909","sensory perception of taste",0.162,2.7258,0.857,0.262,"positive regulation of muscle tissue development"),
c("GO:0045444","fat cell differentiation",0.409,2.7305,0.840,0.265,"positive regulation of muscle tissue development"),
c("GO:0007586","digestion",0.235,2.7352,0.875,0.271,"positive regulation of muscle tissue development"),
c("GO:0002315","marginal zone B cell differentiation",0.002,1.4073,0.835,0.287,"positive regulation of muscle tissue development"),
c("GO:0001503","ossification",0.817,1.7897,0.864,0.302,"positive regulation of muscle tissue development"),
c("GO:0030878","thyroid gland development",0.051,1.8024,0.843,0.304,"positive regulation of muscle tissue development"),
c("GO:0061369","negative regulation of testicular blood vessel morphogenesis",0.001,1.7040,0.819,0.310,"positive regulation of muscle tissue development"),
c("GO:1901857","positive regulation of cellular respiration",0.002,1.4073,0.831,0.315,"positive regulation of muscle tissue development"),
c("GO:0048557","embryonic digestive tract morphogenesis",0.052,1.8024,0.824,0.319,"positive regulation of muscle tissue development"),
c("GO:0021682","nerve maturation",0.009,1.7040,0.867,0.325,"positive regulation of muscle tissue development"),
c("GO:0090341","negative regulation of secretion of lysosomal enzymes",0.010,1.7040,0.807,0.333,"positive regulation of muscle tissue development"),
c("GO:0090407","organophosphate biosynthetic process",2.638,1.5462,0.853,0.339,"positive regulation of muscle tissue development"),
c("GO:0048608","reproductive structure development",1.170,2.4522,0.812,0.357,"positive regulation of muscle tissue development"),
c("GO:0010560","positive regulation of glycoprotein biosynthetic process",0.018,1.8938,0.806,0.358,"positive regulation of muscle tissue development"),
c("GO:0002268","follicular dendritic cell differentiation",0.005,1.4073,0.876,0.370,"positive regulation of muscle tissue development"),
c("GO:0050873","brown fat cell differentiation",0.090,2.1694,0.853,0.371,"positive regulation of muscle tissue development"),
c("GO:2000171","negative regulation of dendrite development",0.007,1.4073,0.731,0.380,"positive regulation of muscle tissue development"),
c("GO:0010870","positive regulation of receptor biosynthetic process",0.013,1.8938,0.824,0.381,"positive regulation of muscle tissue development"),
c("GO:0072075","metanephric mesenchyme development",0.031,1.9974,0.824,0.381,"positive regulation of muscle tissue development"),
c("GO:0002266","follicular dendritic cell activation",0.005,1.4073,0.941,0.383,"positive regulation of muscle tissue development"),
c("GO:0060231","mesenchymal to epithelial transition",0.036,1.8024,0.802,0.385,"positive regulation of muscle tissue development"),
c("GO:0010171","body morphogenesis",0.222,1.4726,0.878,0.387,"positive regulation of muscle tissue development"),
c("GO:0006097","glyoxylate cycle",0.002,1.7040,0.859,0.387,"positive regulation of muscle tissue development"),
c("GO:0014733","regulation of skeletal muscle adaptation",0.013,1.4073,0.831,0.393,"positive regulation of muscle tissue development"),
c("GO:0001993","regulation of systemic arterial blood pressure by norepinephrine-epinephrine",0.019,2.4271,0.791,0.404,"positive regulation of muscle tissue development"),
c("GO:0061183","regulation of dermatome development",0.006,1.7040,0.817,0.409,"positive regulation of muscle tissue development"),
c("GO:0003008","system process",4.235,1.9024,0.845,0.422,"positive regulation of muscle tissue development"),
c("GO:0035270","endocrine system development",0.434,1.8136,0.836,0.423,"positive regulation of muscle tissue development"),
c("GO:0061073","ciliary body morphogenesis",0.009,1.7040,0.857,0.440,"positive regulation of muscle tissue development"),
c("GO:0019520","aldonic acid metabolic process",0.002,1.4073,0.859,0.448,"positive regulation of muscle tissue development"),
c("GO:0019521","D-gluconate metabolic process",0.002,1.4073,0.859,0.448,"positive regulation of muscle tissue development"),
c("GO:0042536","negative regulation of tumor necrosis factor biosynthetic process",0.009,1.7040,0.738,0.449,"positive regulation of muscle tissue development"),
c("GO:0001655","urogenital system development",0.815,1.6765,0.828,0.452,"positive regulation of muscle tissue development"),
c("GO:0060427","lung connective tissue development",0.003,1.7040,0.853,0.455,"positive regulation of muscle tissue development"),
c("GO:0006355","regulation of transcription, DNA-templated",10.156,1.9370,0.754,0.461,"positive regulation of muscle tissue development"),
c("GO:0022600","digestive system process",0.146,1.6061,0.857,0.467,"positive regulation of muscle tissue development"),
c("GO:0061458","reproductive system development",1.184,2.4365,0.823,0.471,"positive regulation of muscle tissue development"),
c("GO:0060764","cell-cell signaling involved in mammary gland development",0.003,1.7040,0.822,0.477,"positive regulation of muscle tissue development"),
c("GO:0048732","gland development",1.335,2.1694,0.813,0.478,"positive regulation of muscle tissue development"),
c("GO:2000181","negative regulation of blood vessel morphogenesis",0.001,1.7040,0.819,0.484,"positive regulation of muscle tissue development"),
c("GO:0048636","positive regulation of muscle organ development",0.038,1.8938,0.786,0.488,"positive regulation of muscle tissue development"),
c("GO:0019637","organophosphate metabolic process",10.352,1.4865,0.874,0.488,"positive regulation of muscle tissue development"),
c("GO:0033504","floor plate development",0.014,1.4073,0.839,0.493,"positive regulation of muscle tissue development"),
c("GO:1900373","positive regulation of purine nucleotide biosynthetic process",0.140,1.5709,0.733,0.507,"positive regulation of muscle tissue development"),
c("GO:0060435","bronchiole development",0.006,1.7040,0.858,0.511,"positive regulation of muscle tissue development"),
c("GO:0060658","nipple morphogenesis",0.007,1.4073,0.856,0.521,"positive regulation of muscle tissue development"),
c("GO:0032613","interleukin-10 production",0.093,1.4626,0.876,0.530,"positive regulation of muscle tissue development"),
c("GO:0006109","regulation of carbohydrate metabolic process",0.300,1.4166,0.853,0.537,"positive regulation of muscle tissue development"),
c("GO:0050968","detection of chemical stimulus involved in sensory perception of pain",0.002,1.4073,0.853,0.538,"positive regulation of muscle tissue development"),
c("GO:0003012","muscle system process",0.830,1.4468,0.845,0.540,"positive regulation of muscle tissue development"),
c("GO:0060618","nipple development",0.007,1.4073,0.859,0.540,"positive regulation of muscle tissue development"),
c("GO:0010460","positive regulation of heart rate",0.038,1.5804,0.758,0.561,"positive regulation of muscle tissue development"),
c("GO:0030237","female sex determination",0.006,1.7040,0.870,0.562,"positive regulation of muscle tissue development"),
c("GO:0060748","tertiary branching involved in mammary gland duct morphogenesis",0.006,1.7040,0.816,0.562,"positive regulation of muscle tissue development"),
c("GO:0061205","paramesonephric duct development",0.006,1.4073,0.859,0.562,"positive regulation of muscle tissue development"),
c("GO:0050915","sensory perception of sour taste",0.006,1.4073,0.882,0.568,"positive regulation of muscle tissue development"),
c("GO:0021960","anterior commissure morphogenesis",0.011,1.4073,0.789,0.578,"positive regulation of muscle tissue development"),
c("GO:2000019","negative regulation of male gonad development",0.002,1.7040,0.806,0.579,"positive regulation of muscle tissue development"),
c("GO:0009880","embryonic pattern specification",0.162,2.1898,0.835,0.604,"positive regulation of muscle tissue development"),
c("GO:0001987","vasoconstriction of artery involved in baroreceptor response to lowering of systemic arterial blood pressure",0.001,1.7040,0.816,0.615,"positive regulation of muscle tissue development"),
c("GO:0061054","dermatome development",0.006,1.7040,0.853,0.623,"positive regulation of muscle tissue development"),
c("GO:0045082","positive regulation of interleukin-10 biosynthetic process",0.003,1.7040,0.744,0.624,"positive regulation of muscle tissue development"),
c("GO:0051490","negative regulation of filopodium assembly",0.009,1.4073,0.823,0.635,"positive regulation of muscle tissue development"),
c("GO:0060126","somatotropin secreting cell differentiation",0.008,1.4073,0.823,0.637,"positive regulation of muscle tissue development"),
c("GO:0072074","kidney mesenchyme development",0.040,1.8024,0.825,0.643,"positive regulation of muscle tissue development"),
c("GO:0060135","maternal process involved in female pregnancy",0.180,1.4421,0.847,0.645,"positive regulation of muscle tissue development"),
c("GO:0072272","proximal/distal pattern formation involved in metanephric nephron development",0.002,1.4073,0.847,0.647,"positive regulation of muscle tissue development"),
c("GO:2001076","positive regulation of metanephric ureteric bud development",0.002,1.4073,0.792,0.647,"positive regulation of muscle tissue development"),
c("GO:0000578","embryonic axis specification",0.089,1.9454,0.839,0.657,"positive regulation of muscle tissue development"),
c("GO:0010563","negative regulation of phosphorus metabolic process",0.841,1.5748,0.783,0.659,"positive regulation of muscle tissue development"),
c("GO:0035947","regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter",0.002,1.4073,0.795,0.663,"positive regulation of muscle tissue development"),
c("GO:0045818","negative regulation of glycogen catabolic process",0.002,1.7040,0.796,0.663,"positive regulation of muscle tissue development"),
c("GO:0045926","negative regulation of growth",0.466,1.6633,0.903,0.671,"positive regulation of muscle tissue development"),
c("GO:0060574","intestinal epithelial cell maturation",0.007,1.4073,0.811,0.672,"positive regulation of muscle tissue development"),
c("GO:1901861","regulation of muscle tissue development",0.317,1.8371,0.829,0.675,"positive regulation of muscle tissue development"),
c("GO:0060993","kidney morphogenesis",0.105,1.7201,0.821,0.679,"positive regulation of muscle tissue development"),
c("GO:0042091","interleukin-10 biosynthetic process",0.005,1.4073,0.846,0.687,"positive regulation of muscle tissue development"),
c("GO:0060538","skeletal muscle organ development",0.498,1.7713,0.815,0.695,"positive regulation of muscle tissue development"),
c("GO:1902170","cellular response to reactive nitrogen species",0.030,3.4089,0.910,0.000,"cellular response to reactive nitrogen species"),
c("GO:0007187","G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger",0.311,2.0985,0.849,0.193,"cellular response to reactive nitrogen species"),
c("GO:0036273","response to statin",0.005,1.4073,0.954,0.246,"cellular response to reactive nitrogen species"),
c("GO:0007264","small GTPase mediated signal transduction",2.633,1.7768,0.825,0.326,"cellular response to reactive nitrogen species"),
c("GO:0071346","cellular response to interferon-gamma",0.224,3.1024,0.890,0.387,"cellular response to reactive nitrogen species"),
c("GO:0080033","response to nitrite",0.001,1.7040,0.945,0.389,"cellular response to reactive nitrogen species"),
c("GO:0002032","desensitization of G-protein coupled receptor protein signaling pathway by arrestin",0.003,1.4073,0.851,0.407,"cellular response to reactive nitrogen species"),
c("GO:0040037","negative regulation of fibroblast growth factor receptor signaling pathway",0.035,1.8024,0.813,0.419,"cellular response to reactive nitrogen species"),
c("GO:0036315","cellular response to sterol",0.036,1.7210,0.900,0.420,"cellular response to reactive nitrogen species"),
c("GO:0070885","negative regulation of calcineurin-NFAT signaling cascade",0.011,1.4073,0.848,0.445,"cellular response to reactive nitrogen species"),
c("GO:0038166","angiotensin-activated signaling pathway",0.014,1.4073,0.875,0.446,"cellular response to reactive nitrogen species"),
c("GO:0070528","protein kinase C signaling",0.072,1.4626,0.866,0.464,"cellular response to reactive nitrogen species"),
c("GO:1901700","response to oxygen-containing compound",3.064,1.6891,0.933,0.466,"cellular response to reactive nitrogen species"),
c("GO:0071875","adrenergic receptor signaling pathway",0.042,1.6474,0.867,0.483,"cellular response to reactive nitrogen species"),
c("GO:0006953","acute-phase response",0.088,1.7615,0.968,0.513,"cellular response to reactive nitrogen species"),
c("GO:0071732","cellular response to nitric oxide",0.015,1.7040,0.897,0.514,"cellular response to reactive nitrogen species"),
c("GO:0030178","negative regulation of Wnt signaling pathway",0.292,1.4684,0.815,0.549,"cellular response to reactive nitrogen species"),
c("GO:0044334","canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition",0.002,1.4073,0.710,0.567,"cellular response to reactive nitrogen species"),
c("GO:1901701","cellular response to oxygen-containing compound",1.893,1.5197,0.875,0.599,"cellular response to reactive nitrogen species"),
c("GO:0036314","response to sterol",0.049,1.4626,0.935,0.621,"cellular response to reactive nitrogen species"),
c("GO:0071731","response to nitric oxide",0.018,1.4073,0.932,0.626,"cellular response to reactive nitrogen species"),
c("GO:0007265","Ras protein signal transduction",1.560,1.4288,0.833,0.647,"cellular response to reactive nitrogen species"),
c("GO:0071322","cellular response to carbohydrate stimulus",0.246,1.6633,0.879,0.677,"cellular response to reactive nitrogen species"),
c("GO:0034341","response to interferon-gamma",0.263,2.5654,0.930,0.687,"cellular response to reactive nitrogen species"),
c("GO:0071332","cellular response to fructose stimulus",0.009,1.4073,0.899,0.690,"cellular response to reactive nitrogen species"),
c("GO:0035725","sodium ion transmembrane transport",0.343,3.3665,0.853,0.030,"sodium ion transmembrane transport"),
c("GO:0036336","dendritic cell migration",0.046,1.8024,0.888,0.202,"sodium ion transmembrane transport"),
c("GO:0045209","MAPK phosphatase export from nucleus, leptomycin B sensitive",0.001,1.7040,0.916,0.203,"sodium ion transmembrane transport"),
c("GO:0042045","epithelial fluid transport",0.007,1.4073,0.930,0.226,"sodium ion transmembrane transport"),
c("GO:0015797","mannitol transport",0.001,1.7040,0.924,0.235,"sodium ion transmembrane transport"),
c("GO:0051181","cofactor transport",0.052,1.4102,0.922,0.261,"sodium ion transmembrane transport"),
c("GO:0051180","vitamin transport",0.077,1.5191,0.920,0.269,"sodium ion transmembrane transport"),
c("GO:0072348","sulfur compound transport",0.103,1.5804,0.919,0.275,"sodium ion transmembrane transport"),
c("GO:0006897","endocytosis",1.430,1.5847,0.925,0.305,"sodium ion transmembrane transport"),
c("GO:0015884","folic acid transport",0.014,2.4271,0.887,0.323,"sodium ion transmembrane transport"),
c("GO:0090088","regulation of oligopeptide transport",0.003,1.4073,0.863,0.406,"sodium ion transmembrane transport"),
c("GO:0070358","actin polymerization-dependent cell motility",0.008,1.4073,0.901,0.417,"sodium ion transmembrane transport"),
c("GO:1900163","positive regulation of phospholipid scramblase activity",0.001,1.7040,0.802,0.455,"sodium ion transmembrane transport"),
c("GO:0015705","iodide transport",0.050,1.4073,0.907,0.484,"sodium ion transmembrane transport"),
c("GO:0006607","NLS-bearing protein import into nucleus",0.030,1.6474,0.902,0.488,"sodium ion transmembrane transport"),
c("GO:0015724","formate transport",0.001,1.7040,0.912,0.490,"sodium ion transmembrane transport"),
c("GO:0045056","transcytosis",0.018,1.4073,0.924,0.515,"sodium ion transmembrane transport"),
c("GO:0016561","protein import into peroxisome matrix, translocation",0.003,1.4073,0.844,0.554,"sodium ion transmembrane transport"),
c("GO:0015672","monovalent inorganic cation transport",4.597,2.2749,0.882,0.594,"sodium ion transmembrane transport"),
c("GO:2000402","negative regulation of lymphocyte migration",0.005,1.4073,0.831,0.594,"sodium ion transmembrane transport"),
c("GO:0002408","myeloid dendritic cell chemotaxis",0.006,1.7040,0.858,0.601,"sodium ion transmembrane transport"),
c("GO:0045208","MAPK phosphatase export from nucleus",0.001,1.7040,0.916,0.606,"sodium ion transmembrane transport"),
c("GO:0051457","maintenance of protein location in nucleus",0.026,1.5804,0.806,0.611,"sodium ion transmembrane transport"),
c("GO:0006811","ion transport",7.803,2.4547,0.888,0.614,"sodium ion transmembrane transport"),
c("GO:0045204","MAPK export from nucleus",0.002,1.7040,0.914,0.625,"sodium ion transmembrane transport"),
c("GO:0046724","oxalic acid secretion",0.002,1.7040,0.903,0.630,"sodium ion transmembrane transport"),
c("GO:0019532","oxalate transport",0.006,1.4073,0.903,0.660,"sodium ion transmembrane transport"),
c("GO:0032417","positive regulation of sodium:proton antiporter activity",0.005,1.4073,0.827,0.664,"sodium ion transmembrane transport"),
c("GO:0072337","modified amino acid transport",0.049,1.5804,0.884,0.668,"sodium ion transmembrane transport"),
c("GO:0006814","sodium ion transport",0.536,2.8761,0.896,0.682,"sodium ion transmembrane transport"),
c("GO:0006909","phagocytosis",0.545,1.5474,0.906,0.699,"sodium ion transmembrane transport"),
c("GO:0042737","drug catabolic process",0.018,2.9393,0.923,0.042,"drug catabolism"),
c("GO:0009822","alkaloid catabolic process",0.003,1.4073,0.916,0.265,"drug catabolism"),
c("GO:0042752","regulation of circadian rhythm",0.179,1.8492,0.951,0.049,"regulation of circadian rhythm"),
c("GO:0009266","response to temperature stimulus",0.307,1.7905,0.975,0.057,"response to temperature stimulus"),
c("GO:0009409","response to cold",0.093,1.9454,0.965,0.580,"response to temperature stimulus"),
c("GO:0070417","cellular response to cold",0.003,1.4073,0.935,0.669,"response to temperature stimulus"),
c("GO:0051764","actin crosslink formation",0.046,2.6440,0.875,0.065,"actin crosslink formation"),
c("GO:0044091","membrane biogenesis",0.044,1.8024,0.936,0.235,"actin crosslink formation"),
c("GO:0043983","histone H4-K12 acetylation",0.014,2.2573,0.832,0.337,"actin crosslink formation"),
c("GO:0035616","histone H2B conserved C-terminal lysine deubiquitination",0.001,1.7040,0.856,0.427,"actin crosslink formation"),
c("GO:0031113","regulation of microtubule polymerization",0.056,2.6271,0.805,0.464,"actin crosslink formation"),
c("GO:0003351","epithelial cilium movement",0.035,1.7210,0.919,0.508,"actin crosslink formation"),
c("GO:0036158","outer dynein arm assembly",0.009,1.4073,0.921,0.536,"actin crosslink formation"),
c("GO:0051639","actin filament network formation",0.003,1.4073,0.892,0.538,"actin crosslink formation"),
c("GO:0032464","positive regulation of protein homooligomerization",0.014,1.8938,0.862,0.632,"actin crosslink formation"),
c("GO:0003341","cilium movement",0.085,1.4102,0.915,0.652,"actin crosslink formation"),
c("GO:0018917","fluorene metabolic process",0.003,1.7040,0.937,0.066,"fluorene metabolism"),
c("GO:0070242","thymocyte apoptotic process",0.073,2.3019,0.910,0.067,"thymocyte apoptotic process"),
c("GO:0070269","pyroptosis",0.003,1.7040,0.928,0.350,"thymocyte apoptotic process"),
c("GO:0012502","induction of programmed cell death",0.007,1.4073,0.859,0.364,"thymocyte apoptotic process"),
c("GO:0006919","activation of cysteine-type endopeptidase activity involved in apoptotic process",0.157,1.9618,0.795,0.450,"thymocyte apoptotic process"),
c("GO:0051186","cofactor metabolic process",0.798,1.7133,0.927,0.074,"cofactor metabolism"),
c("GO:0017144","drug metabolic process",0.048,1.5191,0.939,0.080,"drug metabolism"),
c("GO:0050794","regulation of cellular process",28.971,1.5209,0.900,0.093,"regulation of cellular process"),
c("GO:0043543","protein acylation",0.416,1.8047,0.899,0.097,"protein acylation"));
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# 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:0016340","calcium-dependent cell-matrix adhesion",0.010,1.7040,0.995,0.000,"calcium-dependent cell-matrix adhesion"),
c("GO:0050896","response to stimulus",47.248,1.5715,0.997,0.000,"response to stimulus"),
c("GO:1901615","organic hydroxy compound metabolic process",1.118,4.0809,0.939,0.000,"organic hydroxy compound metabolism"),
c("GO:0006066","alcohol metabolic process",0.738,3.4949,0.845,0.103,"organic hydroxy compound metabolism"),
c("GO:0008209","androgen metabolic process",0.074,3.2518,0.726,0.161,"organic hydroxy compound metabolism"),
c("GO:0006629","lipid metabolic process",3.159,2.5302,0.881,0.234,"organic hydroxy compound metabolism"),
c("GO:0046655","folic acid metabolic process",0.019,2.1163,0.842,0.257,"organic hydroxy compound metabolism"),
c("GO:0006766","vitamin metabolic process",0.209,1.5412,0.892,0.312,"organic hydroxy compound metabolism"),
c("GO:0019048","modulation by virus of host morphology or physiology",0.033,2.2343,0.842,0.318,"organic hydroxy compound metabolism"),
c("GO:0050821","protein stabilization",0.131,3.0223,0.798,0.350,"organic hydroxy compound metabolism"),
c("GO:0002118","aggressive behavior",0.023,1.4073,0.961,0.363,"organic hydroxy compound metabolism"),
c("GO:0046340","diacylglycerol catabolic process",0.006,1.4073,0.816,0.394,"organic hydroxy compound metabolism"),
c("GO:0046490","isopentenyl diphosphate metabolic process",0.006,1.7040,0.820,0.394,"organic hydroxy compound metabolism"),
c("GO:0070143","mitochondrial alanyl-tRNA aminoacylation",0.001,1.7040,0.811,0.410,"organic hydroxy compound metabolism"),
c("GO:0032844","regulation of homeostatic process",0.737,2.4365,0.844,0.419,"organic hydroxy compound metabolism"),
c("GO:1901860","positive regulation of mitochondrial DNA metabolic process",0.002,1.4073,0.806,0.453,"organic hydroxy compound metabolism"),
c("GO:2000505","regulation of energy homeostasis",0.019,2.2573,0.780,0.493,"organic hydroxy compound metabolism"),
c("GO:0010960","magnesium ion homeostasis",0.025,1.4073,0.872,0.503,"organic hydroxy compound metabolism"),
c("GO:0010817","regulation of hormone levels",1.029,1.5748,0.856,0.510,"organic hydroxy compound metabolism"),
c("GO:1901194","negative regulation of formation of translation preinitiation complex",0.001,1.7040,0.793,0.526,"organic hydroxy compound metabolism"),
c("GO:0036112","medium-chain fatty-acyl-CoA metabolic process",0.003,1.7040,0.910,0.534,"organic hydroxy compound metabolism"),
c("GO:0032787","monocarboxylic acid metabolic process",1.329,1.6310,0.824,0.535,"organic hydroxy compound metabolism"),
c("GO:2000189","positive regulation of cholesterol homeostasis",0.007,1.4073,0.865,0.537,"organic hydroxy compound metabolism"),
c("GO:2000754","regulation of sphingomyelin catabolic process",0.001,1.7040,0.745,0.546,"organic hydroxy compound metabolism"),
c("GO:0019264","glycine biosynthetic process from serine",0.014,1.4073,0.829,0.561,"organic hydroxy compound metabolism"),
c("GO:0006419","alanyl-tRNA aminoacylation",0.009,1.4073,0.839,0.569,"organic hydroxy compound metabolism"),
c("GO:0031945","positive regulation of glucocorticoid metabolic process",0.001,1.7040,0.731,0.579,"organic hydroxy compound metabolism"),
c("GO:0001678","cellular glucose homeostasis",0.235,2.3487,0.814,0.606,"organic hydroxy compound metabolism"),
c("GO:0044255","cellular lipid metabolic process",2.183,2.8297,0.768,0.607,"organic hydroxy compound metabolism"),
c("GO:0051454","intracellular pH elevation",0.048,1.7040,0.831,0.626,"organic hydroxy compound metabolism"),
c("GO:0055067","monovalent inorganic cation homeostasis",0.235,1.8983,0.853,0.628,"organic hydroxy compound metabolism"),
c("GO:1901193","regulation of formation of translation preinitiation complex",0.001,1.7040,0.805,0.644,"organic hydroxy compound metabolism"),
c("GO:0016101","diterpenoid metabolic process",0.146,1.8661,0.790,0.646,"organic hydroxy compound metabolism"),
c("GO:0019395","fatty acid oxidation",0.155,1.5621,0.768,0.650,"organic hydroxy compound metabolism"),
c("GO:0001659","temperature homeostasis",0.074,2.0516,0.781,0.654,"organic hydroxy compound metabolism"),
c("GO:2000753","positive regulation of glucosylceramide catabolic process",0.001,1.7040,0.754,0.663,"organic hydroxy compound metabolism"),
c("GO:0033500","carbohydrate homeostasis",0.473,1.8681,0.847,0.667,"organic hydroxy compound metabolism"),
c("GO:2000225","negative regulation of testosterone biosynthetic process",0.001,1.7040,0.692,0.669,"organic hydroxy compound metabolism"),
c("GO:0046889","positive regulation of lipid biosynthetic process",0.108,1.6426,0.727,0.673,"organic hydroxy compound metabolism"),
c("GO:0006720","isoprenoid metabolic process",0.232,1.9618,0.795,0.677,"organic hydroxy compound metabolism"),
c("GO:0097009","energy homeostasis",0.046,1.7210,0.788,0.692,"organic hydroxy compound metabolism"),
c("GO:0044242","cellular lipid catabolic process",0.310,1.6983,0.775,0.697,"organic hydroxy compound metabolism"),
c("GO:1901863","positive regulation of muscle tissue development",0.039,3.0862,0.831,0.000,"positive regulation of muscle tissue development"),
c("GO:0045913","positive regulation of carbohydrate metabolic process",0.112,2.3645,0.826,0.121,"positive regulation of muscle tissue development"),
c("GO:0007379","segment specification",0.027,2.9508,0.856,0.220,"positive regulation of muscle tissue development"),
c("GO:0035265","organ growth",0.300,2.8327,0.870,0.229,"positive regulation of muscle tissue development"),
c("GO:0022038","corpus callosum development",0.025,1.8938,0.853,0.237,"positive regulation of muscle tissue development"),
c("GO:0042326","negative regulation of phosphorylation",0.763,1.8471,0.781,0.244,"positive regulation of muscle tissue development"),
c("GO:0045778","positive regulation of ossification",0.085,1.6807,0.821,0.249,"positive regulation of muscle tissue development"),
c("GO:0050909","sensory perception of taste",0.162,2.7258,0.857,0.262,"positive regulation of muscle tissue development"),
c("GO:0045444","fat cell differentiation",0.409,2.7305,0.840,0.265,"positive regulation of muscle tissue development"),
c("GO:0007586","digestion",0.235,2.7352,0.875,0.271,"positive regulation of muscle tissue development"),
c("GO:0002315","marginal zone B cell differentiation",0.002,1.4073,0.835,0.287,"positive regulation of muscle tissue development"),
c("GO:0001503","ossification",0.817,1.7897,0.864,0.302,"positive regulation of muscle tissue development"),
c("GO:0030878","thyroid gland development",0.051,1.8024,0.843,0.304,"positive regulation of muscle tissue development"),
c("GO:0061369","negative regulation of testicular blood vessel morphogenesis",0.001,1.7040,0.819,0.310,"positive regulation of muscle tissue development"),
c("GO:1901857","positive regulation of cellular respiration",0.002,1.4073,0.831,0.315,"positive regulation of muscle tissue development"),
c("GO:0048557","embryonic digestive tract morphogenesis",0.052,1.8024,0.824,0.319,"positive regulation of muscle tissue development"),
c("GO:0021682","nerve maturation",0.009,1.7040,0.867,0.325,"positive regulation of muscle tissue development"),
c("GO:0090341","negative regulation of secretion of lysosomal enzymes",0.010,1.7040,0.807,0.333,"positive regulation of muscle tissue development"),
c("GO:0090407","organophosphate biosynthetic process",2.638,1.5462,0.853,0.339,"positive regulation of muscle tissue development"),
c("GO:0048608","reproductive structure development",1.170,2.4522,0.812,0.357,"positive regulation of muscle tissue development"),
c("GO:0010560","positive regulation of glycoprotein biosynthetic process",0.018,1.8938,0.806,0.358,"positive regulation of muscle tissue development"),
c("GO:0002268","follicular dendritic cell differentiation",0.005,1.4073,0.876,0.370,"positive regulation of muscle tissue development"),
c("GO:0050873","brown fat cell differentiation",0.090,2.1694,0.853,0.371,"positive regulation of muscle tissue development"),
c("GO:2000171","negative regulation of dendrite development",0.007,1.4073,0.731,0.380,"positive regulation of muscle tissue development"),
c("GO:0010870","positive regulation of receptor biosynthetic process",0.013,1.8938,0.824,0.381,"positive regulation of muscle tissue development"),
c("GO:0072075","metanephric mesenchyme development",0.031,1.9974,0.824,0.381,"positive regulation of muscle tissue development"),
c("GO:0002266","follicular dendritic cell activation",0.005,1.4073,0.941,0.383,"positive regulation of muscle tissue development"),
c("GO:0060231","mesenchymal to epithelial transition",0.036,1.8024,0.802,0.385,"positive regulation of muscle tissue development"),
c("GO:0010171","body morphogenesis",0.222,1.4726,0.878,0.387,"positive regulation of muscle tissue development"),
c("GO:0006097","glyoxylate cycle",0.002,1.7040,0.859,0.387,"positive regulation of muscle tissue development"),
c("GO:0014733","regulation of skeletal muscle adaptation",0.013,1.4073,0.831,0.393,"positive regulation of muscle tissue development"),
c("GO:0001993","regulation of systemic arterial blood pressure by norepinephrine-epinephrine",0.019,2.4271,0.791,0.404,"positive regulation of muscle tissue development"),
c("GO:0061183","regulation of dermatome development",0.006,1.7040,0.817,0.409,"positive regulation of muscle tissue development"),
c("GO:0003008","system process",4.235,1.9024,0.845,0.422,"positive regulation of muscle tissue development"),
c("GO:0035270","endocrine system development",0.434,1.8136,0.836,0.423,"positive regulation of muscle tissue development"),
c("GO:0061073","ciliary body morphogenesis",0.009,1.7040,0.857,0.440,"positive regulation of muscle tissue development"),
c("GO:0019520","aldonic acid metabolic process",0.002,1.4073,0.859,0.448,"positive regulation of muscle tissue development"),
c("GO:0019521","D-gluconate metabolic process",0.002,1.4073,0.859,0.448,"positive regulation of muscle tissue development"),
c("GO:0042536","negative regulation of tumor necrosis factor biosynthetic process",0.009,1.7040,0.738,0.449,"positive regulation of muscle tissue development"),
c("GO:0001655","urogenital system development",0.815,1.6765,0.828,0.452,"positive regulation of muscle tissue development"),
c("GO:0060427","lung connective tissue development",0.003,1.7040,0.853,0.455,"positive regulation of muscle tissue development"),
c("GO:0006355","regulation of transcription, DNA-templated",10.156,1.9370,0.754,0.461,"positive regulation of muscle tissue development"),
c("GO:0022600","digestive system process",0.146,1.6061,0.857,0.467,"positive regulation of muscle tissue development"),
c("GO:0061458","reproductive system development",1.184,2.4365,0.823,0.471,"positive regulation of muscle tissue development"),
c("GO:0060764","cell-cell signaling involved in mammary gland development",0.003,1.7040,0.822,0.477,"positive regulation of muscle tissue development"),
c("GO:0048732","gland development",1.335,2.1694,0.813,0.478,"positive regulation of muscle tissue development"),
c("GO:2000181","negative regulation of blood vessel morphogenesis",0.001,1.7040,0.819,0.484,"positive regulation of muscle tissue development"),
c("GO:0048636","positive regulation of muscle organ development",0.038,1.8938,0.786,0.488,"positive regulation of muscle tissue development"),
c("GO:0019637","organophosphate metabolic process",10.352,1.4865,0.874,0.488,"positive regulation of muscle tissue development"),
c("GO:0033504","floor plate development",0.014,1.4073,0.839,0.493,"positive regulation of muscle tissue development"),
c("GO:1900373","positive regulation of purine nucleotide biosynthetic process",0.140,1.5709,0.733,0.507,"positive regulation of muscle tissue development"),
c("GO:0060435","bronchiole development",0.006,1.7040,0.858,0.511,"positive regulation of muscle tissue development"),
c("GO:0060658","nipple morphogenesis",0.007,1.4073,0.856,0.521,"positive regulation of muscle tissue development"),
c("GO:0032613","interleukin-10 production",0.093,1.4626,0.876,0.530,"positive regulation of muscle tissue development"),
c("GO:0006109","regulation of carbohydrate metabolic process",0.300,1.4166,0.853,0.537,"positive regulation of muscle tissue development"),
c("GO:0050968","detection of chemical stimulus involved in sensory perception of pain",0.002,1.4073,0.853,0.538,"positive regulation of muscle tissue development"),
c("GO:0003012","muscle system process",0.830,1.4468,0.845,0.540,"positive regulation of muscle tissue development"),
c("GO:0060618","nipple development",0.007,1.4073,0.859,0.540,"positive regulation of muscle tissue development"),
c("GO:0010460","positive regulation of heart rate",0.038,1.5804,0.758,0.561,"positive regulation of muscle tissue development"),
c("GO:0030237","female sex determination",0.006,1.7040,0.870,0.562,"positive regulation of muscle tissue development"),
c("GO:0060748","tertiary branching involved in mammary gland duct morphogenesis",0.006,1.7040,0.816,0.562,"positive regulation of muscle tissue development"),
c("GO:0061205","paramesonephric duct development",0.006,1.4073,0.859,0.562,"positive regulation of muscle tissue development"),
c("GO:0050915","sensory perception of sour taste",0.006,1.4073,0.882,0.568,"positive regulation of muscle tissue development"),
c("GO:0021960","anterior commissure morphogenesis",0.011,1.4073,0.789,0.578,"positive regulation of muscle tissue development"),
c("GO:2000019","negative regulation of male gonad development",0.002,1.7040,0.806,0.579,"positive regulation of muscle tissue development"),
c("GO:0009880","embryonic pattern specification",0.162,2.1898,0.835,0.604,"positive regulation of muscle tissue development"),
c("GO:0001987","vasoconstriction of artery involved in baroreceptor response to lowering of systemic arterial blood pressure",0.001,1.7040,0.816,0.615,"positive regulation of muscle tissue development"),
c("GO:0061054","dermatome development",0.006,1.7040,0.853,0.623,"positive regulation of muscle tissue development"),
c("GO:0045082","positive regulation of interleukin-10 biosynthetic process",0.003,1.7040,0.744,0.624,"positive regulation of muscle tissue development"),
c("GO:0051490","negative regulation of filopodium assembly",0.009,1.4073,0.823,0.635,"positive regulation of muscle tissue development"),
c("GO:0060126","somatotropin secreting cell differentiation",0.008,1.4073,0.823,0.637,"positive regulation of muscle tissue development"),
c("GO:0072074","kidney mesenchyme development",0.040,1.8024,0.825,0.643,"positive regulation of muscle tissue development"),
c("GO:0060135","maternal process involved in female pregnancy",0.180,1.4421,0.847,0.645,"positive regulation of muscle tissue development"),
c("GO:0072272","proximal/distal pattern formation involved in metanephric nephron development",0.002,1.4073,0.847,0.647,"positive regulation of muscle tissue development"),
c("GO:2001076","positive regulation of metanephric ureteric bud development",0.002,1.4073,0.792,0.647,"positive regulation of muscle tissue development"),
c("GO:0000578","embryonic axis specification",0.089,1.9454,0.839,0.657,"positive regulation of muscle tissue development"),
c("GO:0010563","negative regulation of phosphorus metabolic process",0.841,1.5748,0.783,0.659,"positive regulation of muscle tissue development"),
c("GO:0035947","regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter",0.002,1.4073,0.795,0.663,"positive regulation of muscle tissue development"),
c("GO:0045818","negative regulation of glycogen catabolic process",0.002,1.7040,0.796,0.663,"positive regulation of muscle tissue development"),
c("GO:0045926","negative regulation of growth",0.466,1.6633,0.903,0.671,"positive regulation of muscle tissue development"),
c("GO:0060574","intestinal epithelial cell maturation",0.007,1.4073,0.811,0.672,"positive regulation of muscle tissue development"),
c("GO:1901861","regulation of muscle tissue development",0.317,1.8371,0.829,0.675,"positive regulation of muscle tissue development"),
c("GO:0060993","kidney morphogenesis",0.105,1.7201,0.821,0.679,"positive regulation of muscle tissue development"),
c("GO:0042091","interleukin-10 biosynthetic process",0.005,1.4073,0.846,0.687,"positive regulation of muscle tissue development"),
c("GO:0060538","skeletal muscle organ development",0.498,1.7713,0.815,0.695,"positive regulation of muscle tissue development"),
c("GO:1902170","cellular response to reactive nitrogen species",0.030,3.4089,0.910,0.000,"cellular response to reactive nitrogen species"),
c("GO:0007187","G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger",0.311,2.0985,0.849,0.193,"cellular response to reactive nitrogen species"),
c("GO:0036273","response to statin",0.005,1.4073,0.954,0.246,"cellular response to reactive nitrogen species"),
c("GO:0007264","small GTPase mediated signal transduction",2.633,1.7768,0.825,0.326,"cellular response to reactive nitrogen species"),
c("GO:0071346","cellular response to interferon-gamma",0.224,3.1024,0.890,0.387,"cellular response to reactive nitrogen species"),
c("GO:0080033","response to nitrite",0.001,1.7040,0.945,0.389,"cellular response to reactive nitrogen species"),
c("GO:0002032","desensitization of G-protein coupled receptor protein signaling pathway by arrestin",0.003,1.4073,0.851,0.407,"cellular response to reactive nitrogen species"),
c("GO:0040037","negative regulation of fibroblast growth factor receptor signaling pathway",0.035,1.8024,0.813,0.419,"cellular response to reactive nitrogen species"),
c("GO:0036315","cellular response to sterol",0.036,1.7210,0.900,0.420,"cellular response to reactive nitrogen species"),
c("GO:0070885","negative regulation of calcineurin-NFAT signaling cascade",0.011,1.4073,0.848,0.445,"cellular response to reactive nitrogen species"),
c("GO:0038166","angiotensin-activated signaling pathway",0.014,1.4073,0.875,0.446,"cellular response to reactive nitrogen species"),
c("GO:0070528","protein kinase C signaling",0.072,1.4626,0.866,0.464,"cellular response to reactive nitrogen species"),
c("GO:1901700","response to oxygen-containing compound",3.064,1.6891,0.933,0.466,"cellular response to reactive nitrogen species"),
c("GO:0071875","adrenergic receptor signaling pathway",0.042,1.6474,0.867,0.483,"cellular response to reactive nitrogen species"),
c("GO:0006953","acute-phase response",0.088,1.7615,0.968,0.513,"cellular response to reactive nitrogen species"),
c("GO:0071732","cellular response to nitric oxide",0.015,1.7040,0.897,0.514,"cellular response to reactive nitrogen species"),
c("GO:0030178","negative regulation of Wnt signaling pathway",0.292,1.4684,0.815,0.549,"cellular response to reactive nitrogen species"),
c("GO:0044334","canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition",0.002,1.4073,0.710,0.567,"cellular response to reactive nitrogen species"),
c("GO:1901701","cellular response to oxygen-containing compound",1.893,1.5197,0.875,0.599,"cellular response to reactive nitrogen species"),
c("GO:0036314","response to sterol",0.049,1.4626,0.935,0.621,"cellular response to reactive nitrogen species"),
c("GO:0071731","response to nitric oxide",0.018,1.4073,0.932,0.626,"cellular response to reactive nitrogen species"),
c("GO:0007265","Ras protein signal transduction",1.560,1.4288,0.833,0.647,"cellular response to reactive nitrogen species"),
c("GO:0071322","cellular response to carbohydrate stimulus",0.246,1.6633,0.879,0.677,"cellular response to reactive nitrogen species"),
c("GO:0034341","response to interferon-gamma",0.263,2.5654,0.930,0.687,"cellular response to reactive nitrogen species"),
c("GO:0071332","cellular response to fructose stimulus",0.009,1.4073,0.899,0.690,"cellular response to reactive nitrogen species"),
c("GO:0035725","sodium ion transmembrane transport",0.343,3.3665,0.853,0.030,"sodium ion transmembrane transport"),
c("GO:0036336","dendritic cell migration",0.046,1.8024,0.888,0.202,"sodium ion transmembrane transport"),
c("GO:0045209","MAPK phosphatase export from nucleus, leptomycin B sensitive",0.001,1.7040,0.916,0.203,"sodium ion transmembrane transport"),
c("GO:0042045","epithelial fluid transport",0.007,1.4073,0.930,0.226,"sodium ion transmembrane transport"),
c("GO:0015797","mannitol transport",0.001,1.7040,0.924,0.235,"sodium ion transmembrane transport"),
c("GO:0051181","cofactor transport",0.052,1.4102,0.922,0.261,"sodium ion transmembrane transport"),
c("GO:0051180","vitamin transport",0.077,1.5191,0.920,0.269,"sodium ion transmembrane transport"),
c("GO:0072348","sulfur compound transport",0.103,1.5804,0.919,0.275,"sodium ion transmembrane transport"),
c("GO:0006897","endocytosis",1.430,1.5847,0.925,0.305,"sodium ion transmembrane transport"),
c("GO:0015884","folic acid transport",0.014,2.4271,0.887,0.323,"sodium ion transmembrane transport"),
c("GO:0090088","regulation of oligopeptide transport",0.003,1.4073,0.863,0.406,"sodium ion transmembrane transport"),
c("GO:0070358","actin polymerization-dependent cell motility",0.008,1.4073,0.901,0.417,"sodium ion transmembrane transport"),
c("GO:1900163","positive regulation of phospholipid scramblase activity",0.001,1.7040,0.802,0.455,"sodium ion transmembrane transport"),
c("GO:0015705","iodide transport",0.050,1.4073,0.907,0.484,"sodium ion transmembrane transport"),
c("GO:0006607","NLS-bearing protein import into nucleus",0.030,1.6474,0.902,0.488,"sodium ion transmembrane transport"),
c("GO:0015724","formate transport",0.001,1.7040,0.912,0.490,"sodium ion transmembrane transport"),
c("GO:0045056","transcytosis",0.018,1.4073,0.924,0.515,"sodium ion transmembrane transport"),
c("GO:0016561","protein import into peroxisome matrix, translocation",0.003,1.4073,0.844,0.554,"sodium ion transmembrane transport"),
c("GO:0015672","monovalent inorganic cation transport",4.597,2.2749,0.882,0.594,"sodium ion transmembrane transport"),
c("GO:2000402","negative regulation of lymphocyte migration",0.005,1.4073,0.831,0.594,"sodium ion transmembrane transport"),
c("GO:0002408","myeloid dendritic cell chemotaxis",0.006,1.7040,0.858,0.601,"sodium ion transmembrane transport"),
c("GO:0045208","MAPK phosphatase export from nucleus",0.001,1.7040,0.916,0.606,"sodium ion transmembrane transport"),
c("GO:0051457","maintenance of protein location in nucleus",0.026,1.5804,0.806,0.611,"sodium ion transmembrane transport"),
c("GO:0006811","ion transport",7.803,2.4547,0.888,0.614,"sodium ion transmembrane transport"),
c("GO:0045204","MAPK export from nucleus",0.002,1.7040,0.914,0.625,"sodium ion transmembrane transport"),
c("GO:0046724","oxalic acid secretion",0.002,1.7040,0.903,0.630,"sodium ion transmembrane transport"),
c("GO:0019532","oxalate transport",0.006,1.4073,0.903,0.660,"sodium ion transmembrane transport"),
c("GO:0032417","positive regulation of sodium:proton antiporter activity",0.005,1.4073,0.827,0.664,"sodium ion transmembrane transport"),
c("GO:0072337","modified amino acid transport",0.049,1.5804,0.884,0.668,"sodium ion transmembrane transport"),
c("GO:0006814","sodium ion transport",0.536,2.8761,0.896,0.682,"sodium ion transmembrane transport"),
c("GO:0006909","phagocytosis",0.545,1.5474,0.906,0.699,"sodium ion transmembrane transport"),
c("GO:0042737","drug catabolic process",0.018,2.9393,0.923,0.042,"drug catabolism"),
c("GO:0009822","alkaloid catabolic process",0.003,1.4073,0.916,0.265,"drug catabolism"),
c("GO:0042752","regulation of circadian rhythm",0.179,1.8492,0.951,0.049,"regulation of circadian rhythm"),
c("GO:0009266","response to temperature stimulus",0.307,1.7905,0.975,0.057,"response to temperature stimulus"),
c("GO:0009409","response to cold",0.093,1.9454,0.965,0.580,"response to temperature stimulus"),
c("GO:0070417","cellular response to cold",0.003,1.4073,0.935,0.669,"response to temperature stimulus"),
c("GO:0051764","actin crosslink formation",0.046,2.6440,0.875,0.065,"actin crosslink formation"),
c("GO:0044091","membrane biogenesis",0.044,1.8024,0.936,0.235,"actin crosslink formation"),
c("GO:0043983","histone H4-K12 acetylation",0.014,2.2573,0.832,0.337,"actin crosslink formation"),
c("GO:0035616","histone H2B conserved C-terminal lysine deubiquitination",0.001,1.7040,0.856,0.427,"actin crosslink formation"),
c("GO:0031113","regulation of microtubule polymerization",0.056,2.6271,0.805,0.464,"actin crosslink formation"),
c("GO:0003351","epithelial cilium movement",0.035,1.7210,0.919,0.508,"actin crosslink formation"),
c("GO:0036158","outer dynein arm assembly",0.009,1.4073,0.921,0.536,"actin crosslink formation"),
c("GO:0051639","actin filament network formation",0.003,1.4073,0.892,0.538,"actin crosslink formation"),
c("GO:0032464","positive regulation of protein homooligomerization",0.014,1.8938,0.862,0.632,"actin crosslink formation"),
c("GO:0003341","cilium movement",0.085,1.4102,0.915,0.652,"actin crosslink formation"),
c("GO:0018917","fluorene metabolic process",0.003,1.7040,0.937,0.066,"fluorene metabolism"),
c("GO:0070242","thymocyte apoptotic process",0.073,2.3019,0.910,0.067,"thymocyte apoptotic process"),
c("GO:0070269","pyroptosis",0.003,1.7040,0.928,0.350,"thymocyte apoptotic process"),
c("GO:0012502","induction of programmed cell death",0.007,1.4073,0.859,0.364,"thymocyte apoptotic process"),
c("GO:0006919","activation of cysteine-type endopeptidase activity involved in apoptotic process",0.157,1.9618,0.795,0.450,"thymocyte apoptotic process"),
c("GO:0051186","cofactor metabolic process",0.798,1.7133,0.927,0.074,"cofactor metabolism"),
c("GO:0017144","drug metabolic process",0.048,1.5191,0.939,0.080,"drug metabolism"),
c("GO:0050794","regulation of cellular process",28.971,1.5209,0.900,0.093,"regulation of cellular process"),
c("GO:0043543","protein acylation",0.416,1.8047,0.899,0.097,"protein acylation"));
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()
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.