inst/extdata/GO/setA-1/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:0002376","immune system process",29.354,1.8182,0.996,0.000,"immune system process"),
c("GO:0003013","circulatory system process",1.113,4.1938,0.829,0.000,"circulatory system process"),
c("GO:0021571","rhombomere 5 development",0.005,3.3768,0.863,0.222,"circulatory system process"),
c("GO:0010260","organ senescence",0.003,1.6260,0.891,0.238,"circulatory system process"),
c("GO:0060426","lung vasculature development",0.016,2.8633,0.877,0.258,"circulatory system process"),
c("GO:0036075","replacement ossification",0.074,1.8207,0.892,0.274,"circulatory system process"),
c("GO:0060712","spongiotrophoblast layer development",0.032,2.2262,0.868,0.287,"circulatory system process"),
c("GO:0044706","multi-multicellular organism process",0.678,3.8861,0.864,0.330,"circulatory system process"),
c("GO:0009888","tissue development",4.199,1.9970,0.927,0.341,"circulatory system process"),
c("GO:0001503","ossification",0.817,2.0434,0.874,0.345,"circulatory system process"),
c("GO:0050817","coagulation",0.929,1.6710,0.873,0.350,"circulatory system process"),
c("GO:0035284","brain segmentation",0.003,3.3768,0.882,0.390,"circulatory system process"),
c("GO:0060730","regulation of intestinal epithelial structure maintenance",0.002,1.9245,0.821,0.399,"circulatory system process"),
c("GO:0021612","facial nerve structural organization",0.022,1.6260,0.871,0.403,"circulatory system process"),
c("GO:0003008","system process",4.235,1.8066,0.855,0.419,"circulatory system process"),
c("GO:0002041","intussusceptive angiogenesis",0.002,1.9245,0.888,0.433,"circulatory system process"),
c("GO:0045906","negative regulation of vasoconstriction",0.006,1.6260,0.782,0.442,"circulatory system process"),
c("GO:0051216","cartilage development",0.566,1.9241,0.845,0.459,"circulatory system process"),
c("GO:0072307","regulation of metanephric nephron tubule epithelial cell differentiation",0.023,1.9245,0.785,0.474,"circulatory system process"),
c("GO:0048646","anatomical structure formation involved in morphogenesis",2.581,1.7701,0.918,0.560,"circulatory system process"),
c("GO:0001944","vasculature development",1.399,2.1537,0.841,0.569,"circulatory system process"),
c("GO:0052097","interspecies quorum sensing",0.435,1.9245,0.845,0.571,"circulatory system process"),
c("GO:0010259","multicellular organismal aging",0.113,1.5943,0.874,0.572,"circulatory system process"),
c("GO:0007565","female pregnancy",0.542,2.7696,0.860,0.583,"circulatory system process"),
c("GO:0035283","central nervous system segmentation",0.003,3.3768,0.886,0.584,"circulatory system process"),
c("GO:0021546","rhombomere development",0.013,2.8633,0.868,0.585,"circulatory system process"),
c("GO:0003018","vascular process in circulatory system",0.436,4.3279,0.822,0.610,"circulatory system process"),
c("GO:0014826","vein smooth muscle contraction",0.005,1.6260,0.807,0.617,"circulatory system process"),
c("GO:0060452","positive regulation of cardiac muscle contraction",0.014,3.0809,0.803,0.621,"circulatory system process"),
c("GO:0030154","cell differentiation",8.015,2.2848,0.843,0.622,"circulatory system process"),
c("GO:0043116","negative regulation of vascular permeability",0.026,2.5467,0.802,0.650,"circulatory system process"),
c("GO:0003012","muscle system process",0.830,2.1135,0.833,0.652,"circulatory system process"),
c("GO:0044057","regulation of system process",1.035,3.3010,0.795,0.668,"circulatory system process"),
c("GO:0010460","positive regulation of heart rate",0.038,1.9978,0.777,0.668,"circulatory system process"),
c("GO:0006936","muscle contraction",0.724,2.4868,0.817,0.687,"circulatory system process"),
c("GO:0009605","response to external stimulus",4.459,3.4815,0.949,0.000,"response to external stimulus"),
c("GO:0006935","chemotaxis",1.276,3.4815,0.772,0.106,"response to external stimulus"),
c("GO:0009607","response to biotic stimulus",1.599,2.5784,0.954,0.109,"response to external stimulus"),
c("GO:0009611","response to wounding",2.056,2.6536,0.944,0.113,"response to external stimulus"),
c("GO:0042221","response to chemical",8.684,5.0506,0.945,0.142,"response to external stimulus"),
c("GO:0006950","response to stress",8.191,1.8245,0.946,0.160,"response to external stimulus"),
c("GO:0051716","cellular response to stimulus",19.092,3.3468,0.899,0.193,"response to external stimulus"),
c("GO:0006955","immune response",27.347,1.8884,0.916,0.268,"response to external stimulus"),
c("GO:0048584","positive regulation of response to stimulus",22.389,1.7508,0.852,0.283,"response to external stimulus"),
c("GO:0034699","response to luteinizing hormone",0.006,1.6260,0.905,0.316,"response to external stimulus"),
c("GO:0042465","kinesis",0.001,1.9245,0.937,0.378,"response to external stimulus"),
c("GO:0042466","chemokinesis",0.001,1.9245,0.937,0.378,"response to external stimulus"),
c("GO:0015893","drug transport",0.060,3.2676,0.831,0.379,"response to external stimulus"),
c("GO:0043278","response to morphine",0.082,1.7696,0.884,0.389,"response to external stimulus"),
c("GO:0070542","response to fatty acid",0.114,3.1739,0.880,0.401,"response to external stimulus"),
c("GO:0070555","response to interleukin-1",0.154,1.6457,0.887,0.412,"response to external stimulus"),
c("GO:0006805","xenobiotic metabolic process",0.218,3.4685,0.815,0.425,"response to external stimulus"),
c("GO:0009410","response to xenobiotic stimulus",0.239,3.3768,0.890,0.429,"response to external stimulus"),
c("GO:0034698","response to gonadotropin",0.082,1.5943,0.887,0.446,"response to external stimulus"),
c("GO:0006970","response to osmotic stress",0.203,1.8710,0.945,0.456,"response to external stimulus"),
c("GO:0033274","response to vitamin B2",0.009,1.6260,0.883,0.471,"response to external stimulus"),
c("GO:0001101","response to acid chemical",0.711,2.7799,0.880,0.480,"response to external stimulus"),
c("GO:0070101","positive regulation of chemokine-mediated signaling pathway",0.003,1.6260,0.799,0.494,"response to external stimulus"),
c("GO:0042493","response to drug",1.179,2.6180,0.875,0.507,"response to external stimulus"),
c("GO:1901654","response to ketone",0.286,2.0857,0.879,0.535,"response to external stimulus"),
c("GO:0007596","blood coagulation",0.909,1.6857,0.772,0.535,"response to external stimulus"),
c("GO:0033993","response to lipid",2.113,2.5686,0.860,0.543,"response to external stimulus"),
c("GO:0006855","drug transmembrane transport",0.044,2.4260,0.811,0.580,"response to external stimulus"),
c("GO:0097530","granulocyte migration",0.147,2.9031,0.779,0.607,"response to external stimulus"),
c("GO:1901700","response to oxygen-containing compound",3.064,2.3036,0.863,0.608,"response to external stimulus"),
c("GO:0031960","response to corticosteroid",0.403,1.8592,0.868,0.614,"response to external stimulus"),
c("GO:0031427","response to methotrexate",0.011,1.6260,0.894,0.619,"response to external stimulus"),
c("GO:0010632","regulation of epithelial cell migration",0.213,1.6688,0.661,0.629,"response to external stimulus"),
c("GO:0007598","blood coagulation, extrinsic pathway",0.006,1.6260,0.786,0.642,"response to external stimulus"),
c("GO:0034201","response to oleic acid",0.023,2.6904,0.893,0.648,"response to external stimulus"),
c("GO:0036293","response to decreased oxygen levels",0.642,1.8595,0.944,0.658,"response to external stimulus"),
c("GO:0034059","response to anoxia",0.007,1.9245,0.954,0.678,"response to external stimulus"),
c("GO:0051385","response to mineralocorticoid",0.088,1.7696,0.882,0.681,"response to external stimulus"),
c("GO:0050900","leukocyte migration",0.509,2.9172,0.794,0.685,"response to external stimulus"),
c("GO:0014070","response to organic cyclic compound",2.318,2.0218,0.859,0.688,"response to external stimulus"),
c("GO:0051707","response to other organism",1.534,2.7352,0.871,0.696,"response to external stimulus"),
c("GO:0070887","cellular response to chemical stimulus",5.433,2.7077,0.796,0.698,"response to external stimulus"),
c("GO:0023052","signaling",17.329,2.1599,0.995,0.000,"signaling"),
c("GO:0040011","locomotion",3.285,2.6421,0.994,0.000,"locomotion"),
c("GO:0044699","single-organism process",71.655,2.3893,0.998,0.000,"single-organism process"),
c("GO:0050896","response to stimulus",47.248,4.3372,0.997,0.000,"response to stimulus"),
c("GO:0051704","multi-organism process",4.431,1.7247,0.995,0.000,"multi-organism process"),
c("GO:0051923","sulfation",0.030,4.0555,0.924,0.000,"sulfation"),
c("GO:0030210","heparin biosynthetic process",0.009,3.0809,0.847,0.559,"sulfation"),
c("GO:0050667","homocysteine metabolic process",0.022,2.8633,0.854,0.588,"sulfation"),
c("GO:0050427","3'-phosphoadenosine 5'-phosphosulfate metabolic process",0.023,3.4815,0.822,0.590,"sulfation"),
c("GO:0030202","heparin metabolic process",0.009,3.0809,0.852,0.624,"sulfation"),
c("GO:0065007","biological regulation",51.216,1.8752,0.997,0.000,"biological regulation"),
c("GO:2001286","regulation of caveolin-mediated endocytosis",0.010,3.8539,0.812,0.024,"regulation of caveolin-mediated endocytosis"),
c("GO:0090166","Golgi disassembly",0.002,1.9245,0.931,0.184,"regulation of caveolin-mediated endocytosis"),
c("GO:0015718","monocarboxylic acid transport",0.270,2.7620,0.874,0.201,"regulation of caveolin-mediated endocytosis"),
c("GO:0030185","nitric oxide transport",0.003,1.9245,0.915,0.213,"regulation of caveolin-mediated endocytosis"),
c("GO:0042045","epithelial fluid transport",0.007,1.6260,0.919,0.223,"regulation of caveolin-mediated endocytosis"),
c("GO:0030198","extracellular matrix organization",0.708,2.0670,0.904,0.259,"regulation of caveolin-mediated endocytosis"),
c("GO:0051674","localization of cell",2.570,2.1500,0.904,0.282,"regulation of caveolin-mediated endocytosis"),
c("GO:0070715","sodium-dependent organic cation transport",0.001,1.9245,0.917,0.310,"regulation of caveolin-mediated endocytosis"),
c("GO:0033624","negative regulation of integrin activation",0.002,1.9245,0.914,0.316,"regulation of caveolin-mediated endocytosis"),
c("GO:0043062","extracellular structure organization",0.709,2.0670,0.904,0.370,"regulation of caveolin-mediated endocytosis"),
c("GO:1901571","fatty acid derivative transport",0.066,1.6345,0.898,0.405,"regulation of caveolin-mediated endocytosis"),
c("GO:0006869","lipid transport",0.732,2.6253,0.873,0.495,"regulation of caveolin-mediated endocytosis"),
c("GO:0015849","organic acid transport",0.681,2.1192,0.880,0.541,"regulation of caveolin-mediated endocytosis"),
c("GO:0010876","lipid localization",0.809,2.2636,0.906,0.557,"regulation of caveolin-mediated endocytosis"),
c("GO:0072584","caveolin-mediated endocytosis",0.017,2.8633,0.912,0.583,"regulation of caveolin-mediated endocytosis"),
c("GO:0006898","receptor-mediated endocytosis",0.534,2.0846,0.896,0.602,"regulation of caveolin-mediated endocytosis"),
c("GO:0070327","thyroid hormone transport",0.003,1.6260,0.842,0.613,"regulation of caveolin-mediated endocytosis"),
c("GO:1902603","carnitine transmembrane transport",0.015,2.3197,0.857,0.674,"regulation of caveolin-mediated endocytosis"),
c("GO:0048259","regulation of receptor-mediated endocytosis",0.099,2.1244,0.789,0.697,"regulation of caveolin-mediated endocytosis"),
c("GO:0006928","cellular component movement",3.830,2.6421,0.912,0.037,"cellular component movement"),
c("GO:0044763","single-organism cellular process",45.302,3.3872,0.921,0.103,"cellular component movement"),
c("GO:0007154","cell communication",17.535,2.0315,0.895,0.173,"cellular component movement"),
c("GO:0006629","lipid metabolic process",3.159,3.6383,0.892,0.047,"lipid metabolism"),
c("GO:1901615","organic hydroxy compound metabolic process",1.118,3.0862,0.944,0.122,"lipid metabolism"),
c("GO:0033609","oxalate metabolic process",0.001,1.9245,0.891,0.132,"lipid metabolism"),
c("GO:0001932","regulation of protein phosphorylation",2.262,2.8013,0.739,0.140,"lipid metabolism"),
c("GO:0006793","phosphorus metabolic process",17.457,3.1308,0.896,0.181,"lipid metabolism"),
c("GO:0032886","regulation of microtubule-based process",0.307,1.8972,0.872,0.184,"lipid metabolism"),
c("GO:1901568","fatty acid derivative metabolic process",0.179,1.5807,0.916,0.200,"lipid metabolism"),
c("GO:0019276","UDP-N-acetylgalactosamine metabolic process",0.003,1.6260,0.877,0.206,"lipid metabolism"),
c("GO:0044264","cellular polysaccharide metabolic process",0.263,1.9987,0.873,0.208,"lipid metabolism"),
c("GO:0043112","receptor metabolic process",0.289,1.7176,0.910,0.210,"lipid metabolism"),
c("GO:0070409","carbamoyl phosphate biosynthetic process",0.014,1.6260,0.902,0.228,"lipid metabolism"),
c("GO:0070408","carbamoyl phosphate metabolic process",0.014,1.6260,0.910,0.229,"lipid metabolism"),
c("GO:0008202","steroid metabolic process",0.613,2.3170,0.886,0.229,"lipid metabolism"),
c("GO:0050651","dermatan sulfate proteoglycan biosynthetic process",0.017,1.9978,0.898,0.236,"lipid metabolism"),
c("GO:0033865","nucleoside bisphosphate metabolic process",0.072,2.4089,0.854,0.263,"lipid metabolism"),
c("GO:0044283","small molecule biosynthetic process",1.120,2.3325,0.876,0.295,"lipid metabolism"),
c("GO:1901566","organonitrogen compound biosynthetic process",2.941,2.1605,0.906,0.335,"lipid metabolism"),
c("GO:1901564","organonitrogen compound metabolic process",11.844,1.8716,0.919,0.344,"lipid metabolism"),
c("GO:0044281","small molecule metabolic process",13.539,1.6704,0.887,0.358,"lipid metabolism"),
c("GO:0051338","regulation of transferase activity",1.829,1.6057,0.871,0.365,"lipid metabolism"),
c("GO:0006576","cellular biogenic amine metabolic process",0.227,1.9169,0.912,0.391,"lipid metabolism"),
c("GO:0044711","single-organism biosynthetic process",4.776,1.6868,0.889,0.409,"lipid metabolism"),
c("GO:0009308","amine metabolic process",0.369,1.8359,0.932,0.412,"lipid metabolism"),
c("GO:0042866","pyruvate biosynthetic process",0.008,1.6260,0.865,0.416,"lipid metabolism"),
c("GO:0006082","organic acid metabolic process",3.105,1.9311,0.836,0.434,"lipid metabolism"),
c("GO:1901676","positive regulation of histone H3-K27 acetylation",0.001,1.9245,0.814,0.460,"lipid metabolism"),
c("GO:0051246","regulation of protein metabolic process",4.423,1.6057,0.840,0.473,"lipid metabolism"),
c("GO:0043651","linoleic acid metabolic process",0.014,2.2262,0.858,0.478,"lipid metabolism"),
c("GO:0046337","phosphatidylethanolamine metabolic process",0.022,2.0670,0.863,0.495,"lipid metabolism"),
c("GO:0046338","phosphatidylethanolamine catabolic process",0.001,1.9245,0.868,0.507,"lipid metabolism"),
c("GO:0000165","MAPK cascade",1.448,2.0830,0.735,0.512,"lipid metabolism"),
c("GO:0030953","astral microtubule organization",0.008,1.6260,0.921,0.515,"lipid metabolism"),
c("GO:0023014","signal transduction by phosphorylation",1.554,1.9702,0.743,0.517,"lipid metabolism"),
c("GO:0006796","phosphate-containing compound metabolic process",17.353,3.2840,0.850,0.520,"lipid metabolism"),
c("GO:0008210","estrogen metabolic process",0.049,2.0670,0.827,0.526,"lipid metabolism"),
c("GO:0043436","oxoacid metabolic process",3.077,1.9686,0.812,0.544,"lipid metabolism"),
c("GO:0033141","positive regulation of peptidyl-serine phosphorylation of STAT protein",0.022,1.6260,0.753,0.570,"lipid metabolism"),
c("GO:0030148","sphingolipid biosynthetic process",0.134,1.6236,0.847,0.572,"lipid metabolism"),
c("GO:0005976","polysaccharide metabolic process",0.292,1.8222,0.915,0.575,"lipid metabolism"),
c("GO:0031122","cytoplasmic microtubule organization",0.062,1.7219,0.911,0.595,"lipid metabolism"),
c("GO:0032436","positive regulation of proteasomal ubiquitin-dependent protein catabolic process",0.106,2.1605,0.783,0.614,"lipid metabolism"),
c("GO:0043974","histone H3-K27 acetylation",0.002,1.6260,0.870,0.617,"lipid metabolism"),
c("GO:0006468","protein phosphorylation",5.136,3.2840,0.820,0.620,"lipid metabolism"),
c("GO:0010563","negative regulation of phosphorus metabolic process",0.841,2.0066,0.780,0.675,"lipid metabolism"),
c("GO:0045936","negative regulation of phosphate metabolic process",0.841,2.0066,0.777,0.677,"lipid metabolism"),
c("GO:0006690","icosanoid metabolic process",0.179,1.5807,0.847,0.686,"lipid metabolism"),
c("GO:0033559","unsaturated fatty acid metabolic process",0.193,2.1555,0.833,0.691,"lipid metabolism"),
c("GO:0023057","negative regulation of signaling",2.197,2.6383,0.846,0.054,"negative regulation of signaling"),
c("GO:0065008","regulation of biological quality",7.337,2.6556,0.937,0.102,"negative regulation of signaling"),
c("GO:0048518","positive regulation of biological process",28.712,1.6155,0.922,0.169,"negative regulation of signaling"),
c("GO:0031583","phospholipase D-activating G-protein coupled receptor signaling pathway",0.002,1.9245,0.875,0.200,"negative regulation of signaling"),
c("GO:0038203","TORC2 signaling",0.010,1.9245,0.863,0.223,"negative regulation of signaling"),
c("GO:0048014","Tie signaling pathway",0.010,1.9245,0.865,0.223,"negative regulation of signaling"),
c("GO:0042313","protein kinase C deactivation",0.001,1.9245,0.869,0.335,"negative regulation of signaling"),
c("GO:0043179","rhythmic excitation",0.007,1.9245,0.881,0.379,"negative regulation of signaling"),
c("GO:0007181","transforming growth factor beta receptor complex assembly",0.005,1.6260,0.803,0.382,"negative regulation of signaling"),
c("GO:0007186","G-protein coupled receptor signaling pathway",3.393,1.5759,0.787,0.402,"negative regulation of signaling"),
c("GO:0042347","negative regulation of NF-kappaB import into nucleus",0.030,2.0670,0.743,0.426,"negative regulation of signaling"),
c("GO:0015697","quaternary ammonium group transport",0.027,1.9978,0.904,0.477,"negative regulation of signaling"),
c("GO:0035556","intracellular signal transduction",6.704,2.7959,0.774,0.505,"negative regulation of signaling"),
c("GO:0051051","negative regulation of transport",0.706,2.5157,0.809,0.512,"negative regulation of signaling"),
c("GO:1902306","negative regulation of sodium ion transmembrane transport",0.002,1.9245,0.821,0.523,"negative regulation of signaling"),
c("GO:0010646","regulation of cell communication",6.570,1.6784,0.818,0.529,"negative regulation of signaling"),
c("GO:0023051","regulation of signaling",6.570,1.6849,0.879,0.534,"negative regulation of signaling"),
c("GO:0008277","regulation of G-protein coupled receptor protein signaling pathway",0.358,1.7011,0.810,0.538,"negative regulation of signaling"),
c("GO:1901017","negative regulation of potassium ion transmembrane transporter activity",0.013,1.9245,0.797,0.575,"negative regulation of signaling"),
c("GO:0010648","negative regulation of cell communication",2.203,2.6180,0.798,0.588,"negative regulation of signaling"),
c("GO:0048585","negative regulation of response to stimulus",2.501,2.1675,0.863,0.598,"negative regulation of signaling"),
c("GO:0007165","signal transduction",16.054,2.3706,0.751,0.640,"negative regulation of signaling"),
c("GO:0051270","regulation of cellular component movement",1.289,1.7462,0.745,0.646,"negative regulation of signaling"),
c("GO:0009968","negative regulation of signal transduction",2.090,2.3449,0.759,0.662,"negative regulation of signaling"),
c("GO:0007166","cell surface receptor signaling pathway",8.919,1.9876,0.767,0.683,"negative regulation of signaling"),
c("GO:0055078","sodium ion homeostasis",0.081,2.0670,0.898,0.060,"sodium ion homeostasis"),
c("GO:0010817","regulation of hormone levels",1.029,2.0066,0.892,0.414,"sodium ion homeostasis"),
c("GO:0090066","regulation of anatomical structure size",0.957,1.7036,0.892,0.525,"sodium ion homeostasis"),
c("GO:0030644","cellular chloride ion homeostasis",0.015,1.6260,0.871,0.526,"sodium ion homeostasis"),
c("GO:0055081","anion homeostasis",0.072,1.6770,0.900,0.584,"sodium ion homeostasis"),
c("GO:0002268","follicular dendritic cell differentiation",0.005,1.6260,0.908,0.065,"follicular dendritic cell differentiation"),
c("GO:0002266","follicular dendritic cell activation",0.005,1.6260,0.944,0.383,"follicular dendritic cell differentiation"),
c("GO:0006790","sulfur compound metabolic process",0.742,3.0132,0.925,0.077,"sulfur compound metabolism"),
c("GO:0009812","flavonoid metabolic process",0.019,2.5467,0.958,0.081,"flavonoid metabolism"),
c("GO:1901616","organic hydroxy compound catabolic process",0.134,2.9431,0.911,0.096,"organic hydroxy compound catabolism"),
c("GO:0046185","aldehyde catabolic process",0.026,2.6904,0.879,0.326,"organic hydroxy compound catabolism"),
c("GO:0044282","small molecule catabolic process",0.575,1.7124,0.874,0.407,"organic hydroxy compound catabolism"),
c("GO:0046164","alcohol catabolic process",0.103,2.1605,0.865,0.659,"organic hydroxy compound catabolism"),
c("GO:0006584","catecholamine metabolic process",0.123,1.6345,0.894,0.668,"organic hydroxy compound catabolism"));
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:0002376","immune system process",29.354,1.8182,0.996,0.000,"immune system process"),
c("GO:0003013","circulatory system process",1.113,4.1938,0.829,0.000,"circulatory system process"),
c("GO:0021571","rhombomere 5 development",0.005,3.3768,0.863,0.222,"circulatory system process"),
c("GO:0010260","organ senescence",0.003,1.6260,0.891,0.238,"circulatory system process"),
c("GO:0060426","lung vasculature development",0.016,2.8633,0.877,0.258,"circulatory system process"),
c("GO:0036075","replacement ossification",0.074,1.8207,0.892,0.274,"circulatory system process"),
c("GO:0060712","spongiotrophoblast layer development",0.032,2.2262,0.868,0.287,"circulatory system process"),
c("GO:0044706","multi-multicellular organism process",0.678,3.8861,0.864,0.330,"circulatory system process"),
c("GO:0009888","tissue development",4.199,1.9970,0.927,0.341,"circulatory system process"),
c("GO:0001503","ossification",0.817,2.0434,0.874,0.345,"circulatory system process"),
c("GO:0050817","coagulation",0.929,1.6710,0.873,0.350,"circulatory system process"),
c("GO:0035284","brain segmentation",0.003,3.3768,0.882,0.390,"circulatory system process"),
c("GO:0060730","regulation of intestinal epithelial structure maintenance",0.002,1.9245,0.821,0.399,"circulatory system process"),
c("GO:0021612","facial nerve structural organization",0.022,1.6260,0.871,0.403,"circulatory system process"),
c("GO:0003008","system process",4.235,1.8066,0.855,0.419,"circulatory system process"),
c("GO:0002041","intussusceptive angiogenesis",0.002,1.9245,0.888,0.433,"circulatory system process"),
c("GO:0045906","negative regulation of vasoconstriction",0.006,1.6260,0.782,0.442,"circulatory system process"),
c("GO:0051216","cartilage development",0.566,1.9241,0.845,0.459,"circulatory system process"),
c("GO:0072307","regulation of metanephric nephron tubule epithelial cell differentiation",0.023,1.9245,0.785,0.474,"circulatory system process"),
c("GO:0048646","anatomical structure formation involved in morphogenesis",2.581,1.7701,0.918,0.560,"circulatory system process"),
c("GO:0001944","vasculature development",1.399,2.1537,0.841,0.569,"circulatory system process"),
c("GO:0052097","interspecies quorum sensing",0.435,1.9245,0.845,0.571,"circulatory system process"),
c("GO:0010259","multicellular organismal aging",0.113,1.5943,0.874,0.572,"circulatory system process"),
c("GO:0007565","female pregnancy",0.542,2.7696,0.860,0.583,"circulatory system process"),
c("GO:0035283","central nervous system segmentation",0.003,3.3768,0.886,0.584,"circulatory system process"),
c("GO:0021546","rhombomere development",0.013,2.8633,0.868,0.585,"circulatory system process"),
c("GO:0003018","vascular process in circulatory system",0.436,4.3279,0.822,0.610,"circulatory system process"),
c("GO:0014826","vein smooth muscle contraction",0.005,1.6260,0.807,0.617,"circulatory system process"),
c("GO:0060452","positive regulation of cardiac muscle contraction",0.014,3.0809,0.803,0.621,"circulatory system process"),
c("GO:0030154","cell differentiation",8.015,2.2848,0.843,0.622,"circulatory system process"),
c("GO:0043116","negative regulation of vascular permeability",0.026,2.5467,0.802,0.650,"circulatory system process"),
c("GO:0003012","muscle system process",0.830,2.1135,0.833,0.652,"circulatory system process"),
c("GO:0044057","regulation of system process",1.035,3.3010,0.795,0.668,"circulatory system process"),
c("GO:0010460","positive regulation of heart rate",0.038,1.9978,0.777,0.668,"circulatory system process"),
c("GO:0006936","muscle contraction",0.724,2.4868,0.817,0.687,"circulatory system process"),
c("GO:0009605","response to external stimulus",4.459,3.4815,0.949,0.000,"response to external stimulus"),
c("GO:0006935","chemotaxis",1.276,3.4815,0.772,0.106,"response to external stimulus"),
c("GO:0009607","response to biotic stimulus",1.599,2.5784,0.954,0.109,"response to external stimulus"),
c("GO:0009611","response to wounding",2.056,2.6536,0.944,0.113,"response to external stimulus"),
c("GO:0042221","response to chemical",8.684,5.0506,0.945,0.142,"response to external stimulus"),
c("GO:0006950","response to stress",8.191,1.8245,0.946,0.160,"response to external stimulus"),
c("GO:0051716","cellular response to stimulus",19.092,3.3468,0.899,0.193,"response to external stimulus"),
c("GO:0006955","immune response",27.347,1.8884,0.916,0.268,"response to external stimulus"),
c("GO:0048584","positive regulation of response to stimulus",22.389,1.7508,0.852,0.283,"response to external stimulus"),
c("GO:0034699","response to luteinizing hormone",0.006,1.6260,0.905,0.316,"response to external stimulus"),
c("GO:0042465","kinesis",0.001,1.9245,0.937,0.378,"response to external stimulus"),
c("GO:0042466","chemokinesis",0.001,1.9245,0.937,0.378,"response to external stimulus"),
c("GO:0015893","drug transport",0.060,3.2676,0.831,0.379,"response to external stimulus"),
c("GO:0043278","response to morphine",0.082,1.7696,0.884,0.389,"response to external stimulus"),
c("GO:0070542","response to fatty acid",0.114,3.1739,0.880,0.401,"response to external stimulus"),
c("GO:0070555","response to interleukin-1",0.154,1.6457,0.887,0.412,"response to external stimulus"),
c("GO:0006805","xenobiotic metabolic process",0.218,3.4685,0.815,0.425,"response to external stimulus"),
c("GO:0009410","response to xenobiotic stimulus",0.239,3.3768,0.890,0.429,"response to external stimulus"),
c("GO:0034698","response to gonadotropin",0.082,1.5943,0.887,0.446,"response to external stimulus"),
c("GO:0006970","response to osmotic stress",0.203,1.8710,0.945,0.456,"response to external stimulus"),
c("GO:0033274","response to vitamin B2",0.009,1.6260,0.883,0.471,"response to external stimulus"),
c("GO:0001101","response to acid chemical",0.711,2.7799,0.880,0.480,"response to external stimulus"),
c("GO:0070101","positive regulation of chemokine-mediated signaling pathway",0.003,1.6260,0.799,0.494,"response to external stimulus"),
c("GO:0042493","response to drug",1.179,2.6180,0.875,0.507,"response to external stimulus"),
c("GO:1901654","response to ketone",0.286,2.0857,0.879,0.535,"response to external stimulus"),
c("GO:0007596","blood coagulation",0.909,1.6857,0.772,0.535,"response to external stimulus"),
c("GO:0033993","response to lipid",2.113,2.5686,0.860,0.543,"response to external stimulus"),
c("GO:0006855","drug transmembrane transport",0.044,2.4260,0.811,0.580,"response to external stimulus"),
c("GO:0097530","granulocyte migration",0.147,2.9031,0.779,0.607,"response to external stimulus"),
c("GO:1901700","response to oxygen-containing compound",3.064,2.3036,0.863,0.608,"response to external stimulus"),
c("GO:0031960","response to corticosteroid",0.403,1.8592,0.868,0.614,"response to external stimulus"),
c("GO:0031427","response to methotrexate",0.011,1.6260,0.894,0.619,"response to external stimulus"),
c("GO:0010632","regulation of epithelial cell migration",0.213,1.6688,0.661,0.629,"response to external stimulus"),
c("GO:0007598","blood coagulation, extrinsic pathway",0.006,1.6260,0.786,0.642,"response to external stimulus"),
c("GO:0034201","response to oleic acid",0.023,2.6904,0.893,0.648,"response to external stimulus"),
c("GO:0036293","response to decreased oxygen levels",0.642,1.8595,0.944,0.658,"response to external stimulus"),
c("GO:0034059","response to anoxia",0.007,1.9245,0.954,0.678,"response to external stimulus"),
c("GO:0051385","response to mineralocorticoid",0.088,1.7696,0.882,0.681,"response to external stimulus"),
c("GO:0050900","leukocyte migration",0.509,2.9172,0.794,0.685,"response to external stimulus"),
c("GO:0014070","response to organic cyclic compound",2.318,2.0218,0.859,0.688,"response to external stimulus"),
c("GO:0051707","response to other organism",1.534,2.7352,0.871,0.696,"response to external stimulus"),
c("GO:0070887","cellular response to chemical stimulus",5.433,2.7077,0.796,0.698,"response to external stimulus"),
c("GO:0023052","signaling",17.329,2.1599,0.995,0.000,"signaling"),
c("GO:0040011","locomotion",3.285,2.6421,0.994,0.000,"locomotion"),
c("GO:0044699","single-organism process",71.655,2.3893,0.998,0.000,"single-organism process"),
c("GO:0050896","response to stimulus",47.248,4.3372,0.997,0.000,"response to stimulus"),
c("GO:0051704","multi-organism process",4.431,1.7247,0.995,0.000,"multi-organism process"),
c("GO:0051923","sulfation",0.030,4.0555,0.924,0.000,"sulfation"),
c("GO:0030210","heparin biosynthetic process",0.009,3.0809,0.847,0.559,"sulfation"),
c("GO:0050667","homocysteine metabolic process",0.022,2.8633,0.854,0.588,"sulfation"),
c("GO:0050427","3'-phosphoadenosine 5'-phosphosulfate metabolic process",0.023,3.4815,0.822,0.590,"sulfation"),
c("GO:0030202","heparin metabolic process",0.009,3.0809,0.852,0.624,"sulfation"),
c("GO:0065007","biological regulation",51.216,1.8752,0.997,0.000,"biological regulation"),
c("GO:2001286","regulation of caveolin-mediated endocytosis",0.010,3.8539,0.812,0.024,"regulation of caveolin-mediated endocytosis"),
c("GO:0090166","Golgi disassembly",0.002,1.9245,0.931,0.184,"regulation of caveolin-mediated endocytosis"),
c("GO:0015718","monocarboxylic acid transport",0.270,2.7620,0.874,0.201,"regulation of caveolin-mediated endocytosis"),
c("GO:0030185","nitric oxide transport",0.003,1.9245,0.915,0.213,"regulation of caveolin-mediated endocytosis"),
c("GO:0042045","epithelial fluid transport",0.007,1.6260,0.919,0.223,"regulation of caveolin-mediated endocytosis"),
c("GO:0030198","extracellular matrix organization",0.708,2.0670,0.904,0.259,"regulation of caveolin-mediated endocytosis"),
c("GO:0051674","localization of cell",2.570,2.1500,0.904,0.282,"regulation of caveolin-mediated endocytosis"),
c("GO:0070715","sodium-dependent organic cation transport",0.001,1.9245,0.917,0.310,"regulation of caveolin-mediated endocytosis"),
c("GO:0033624","negative regulation of integrin activation",0.002,1.9245,0.914,0.316,"regulation of caveolin-mediated endocytosis"),
c("GO:0043062","extracellular structure organization",0.709,2.0670,0.904,0.370,"regulation of caveolin-mediated endocytosis"),
c("GO:1901571","fatty acid derivative transport",0.066,1.6345,0.898,0.405,"regulation of caveolin-mediated endocytosis"),
c("GO:0006869","lipid transport",0.732,2.6253,0.873,0.495,"regulation of caveolin-mediated endocytosis"),
c("GO:0015849","organic acid transport",0.681,2.1192,0.880,0.541,"regulation of caveolin-mediated endocytosis"),
c("GO:0010876","lipid localization",0.809,2.2636,0.906,0.557,"regulation of caveolin-mediated endocytosis"),
c("GO:0072584","caveolin-mediated endocytosis",0.017,2.8633,0.912,0.583,"regulation of caveolin-mediated endocytosis"),
c("GO:0006898","receptor-mediated endocytosis",0.534,2.0846,0.896,0.602,"regulation of caveolin-mediated endocytosis"),
c("GO:0070327","thyroid hormone transport",0.003,1.6260,0.842,0.613,"regulation of caveolin-mediated endocytosis"),
c("GO:1902603","carnitine transmembrane transport",0.015,2.3197,0.857,0.674,"regulation of caveolin-mediated endocytosis"),
c("GO:0048259","regulation of receptor-mediated endocytosis",0.099,2.1244,0.789,0.697,"regulation of caveolin-mediated endocytosis"),
c("GO:0006928","cellular component movement",3.830,2.6421,0.912,0.037,"cellular component movement"),
c("GO:0044763","single-organism cellular process",45.302,3.3872,0.921,0.103,"cellular component movement"),
c("GO:0007154","cell communication",17.535,2.0315,0.895,0.173,"cellular component movement"),
c("GO:0006629","lipid metabolic process",3.159,3.6383,0.892,0.047,"lipid metabolism"),
c("GO:1901615","organic hydroxy compound metabolic process",1.118,3.0862,0.944,0.122,"lipid metabolism"),
c("GO:0033609","oxalate metabolic process",0.001,1.9245,0.891,0.132,"lipid metabolism"),
c("GO:0001932","regulation of protein phosphorylation",2.262,2.8013,0.739,0.140,"lipid metabolism"),
c("GO:0006793","phosphorus metabolic process",17.457,3.1308,0.896,0.181,"lipid metabolism"),
c("GO:0032886","regulation of microtubule-based process",0.307,1.8972,0.872,0.184,"lipid metabolism"),
c("GO:1901568","fatty acid derivative metabolic process",0.179,1.5807,0.916,0.200,"lipid metabolism"),
c("GO:0019276","UDP-N-acetylgalactosamine metabolic process",0.003,1.6260,0.877,0.206,"lipid metabolism"),
c("GO:0044264","cellular polysaccharide metabolic process",0.263,1.9987,0.873,0.208,"lipid metabolism"),
c("GO:0043112","receptor metabolic process",0.289,1.7176,0.910,0.210,"lipid metabolism"),
c("GO:0070409","carbamoyl phosphate biosynthetic process",0.014,1.6260,0.902,0.228,"lipid metabolism"),
c("GO:0070408","carbamoyl phosphate metabolic process",0.014,1.6260,0.910,0.229,"lipid metabolism"),
c("GO:0008202","steroid metabolic process",0.613,2.3170,0.886,0.229,"lipid metabolism"),
c("GO:0050651","dermatan sulfate proteoglycan biosynthetic process",0.017,1.9978,0.898,0.236,"lipid metabolism"),
c("GO:0033865","nucleoside bisphosphate metabolic process",0.072,2.4089,0.854,0.263,"lipid metabolism"),
c("GO:0044283","small molecule biosynthetic process",1.120,2.3325,0.876,0.295,"lipid metabolism"),
c("GO:1901566","organonitrogen compound biosynthetic process",2.941,2.1605,0.906,0.335,"lipid metabolism"),
c("GO:1901564","organonitrogen compound metabolic process",11.844,1.8716,0.919,0.344,"lipid metabolism"),
c("GO:0044281","small molecule metabolic process",13.539,1.6704,0.887,0.358,"lipid metabolism"),
c("GO:0051338","regulation of transferase activity",1.829,1.6057,0.871,0.365,"lipid metabolism"),
c("GO:0006576","cellular biogenic amine metabolic process",0.227,1.9169,0.912,0.391,"lipid metabolism"),
c("GO:0044711","single-organism biosynthetic process",4.776,1.6868,0.889,0.409,"lipid metabolism"),
c("GO:0009308","amine metabolic process",0.369,1.8359,0.932,0.412,"lipid metabolism"),
c("GO:0042866","pyruvate biosynthetic process",0.008,1.6260,0.865,0.416,"lipid metabolism"),
c("GO:0006082","organic acid metabolic process",3.105,1.9311,0.836,0.434,"lipid metabolism"),
c("GO:1901676","positive regulation of histone H3-K27 acetylation",0.001,1.9245,0.814,0.460,"lipid metabolism"),
c("GO:0051246","regulation of protein metabolic process",4.423,1.6057,0.840,0.473,"lipid metabolism"),
c("GO:0043651","linoleic acid metabolic process",0.014,2.2262,0.858,0.478,"lipid metabolism"),
c("GO:0046337","phosphatidylethanolamine metabolic process",0.022,2.0670,0.863,0.495,"lipid metabolism"),
c("GO:0046338","phosphatidylethanolamine catabolic process",0.001,1.9245,0.868,0.507,"lipid metabolism"),
c("GO:0000165","MAPK cascade",1.448,2.0830,0.735,0.512,"lipid metabolism"),
c("GO:0030953","astral microtubule organization",0.008,1.6260,0.921,0.515,"lipid metabolism"),
c("GO:0023014","signal transduction by phosphorylation",1.554,1.9702,0.743,0.517,"lipid metabolism"),
c("GO:0006796","phosphate-containing compound metabolic process",17.353,3.2840,0.850,0.520,"lipid metabolism"),
c("GO:0008210","estrogen metabolic process",0.049,2.0670,0.827,0.526,"lipid metabolism"),
c("GO:0043436","oxoacid metabolic process",3.077,1.9686,0.812,0.544,"lipid metabolism"),
c("GO:0033141","positive regulation of peptidyl-serine phosphorylation of STAT protein",0.022,1.6260,0.753,0.570,"lipid metabolism"),
c("GO:0030148","sphingolipid biosynthetic process",0.134,1.6236,0.847,0.572,"lipid metabolism"),
c("GO:0005976","polysaccharide metabolic process",0.292,1.8222,0.915,0.575,"lipid metabolism"),
c("GO:0031122","cytoplasmic microtubule organization",0.062,1.7219,0.911,0.595,"lipid metabolism"),
c("GO:0032436","positive regulation of proteasomal ubiquitin-dependent protein catabolic process",0.106,2.1605,0.783,0.614,"lipid metabolism"),
c("GO:0043974","histone H3-K27 acetylation",0.002,1.6260,0.870,0.617,"lipid metabolism"),
c("GO:0006468","protein phosphorylation",5.136,3.2840,0.820,0.620,"lipid metabolism"),
c("GO:0010563","negative regulation of phosphorus metabolic process",0.841,2.0066,0.780,0.675,"lipid metabolism"),
c("GO:0045936","negative regulation of phosphate metabolic process",0.841,2.0066,0.777,0.677,"lipid metabolism"),
c("GO:0006690","icosanoid metabolic process",0.179,1.5807,0.847,0.686,"lipid metabolism"),
c("GO:0033559","unsaturated fatty acid metabolic process",0.193,2.1555,0.833,0.691,"lipid metabolism"),
c("GO:0023057","negative regulation of signaling",2.197,2.6383,0.846,0.054,"negative regulation of signaling"),
c("GO:0065008","regulation of biological quality",7.337,2.6556,0.937,0.102,"negative regulation of signaling"),
c("GO:0048518","positive regulation of biological process",28.712,1.6155,0.922,0.169,"negative regulation of signaling"),
c("GO:0031583","phospholipase D-activating G-protein coupled receptor signaling pathway",0.002,1.9245,0.875,0.200,"negative regulation of signaling"),
c("GO:0038203","TORC2 signaling",0.010,1.9245,0.863,0.223,"negative regulation of signaling"),
c("GO:0048014","Tie signaling pathway",0.010,1.9245,0.865,0.223,"negative regulation of signaling"),
c("GO:0042313","protein kinase C deactivation",0.001,1.9245,0.869,0.335,"negative regulation of signaling"),
c("GO:0043179","rhythmic excitation",0.007,1.9245,0.881,0.379,"negative regulation of signaling"),
c("GO:0007181","transforming growth factor beta receptor complex assembly",0.005,1.6260,0.803,0.382,"negative regulation of signaling"),
c("GO:0007186","G-protein coupled receptor signaling pathway",3.393,1.5759,0.787,0.402,"negative regulation of signaling"),
c("GO:0042347","negative regulation of NF-kappaB import into nucleus",0.030,2.0670,0.743,0.426,"negative regulation of signaling"),
c("GO:0015697","quaternary ammonium group transport",0.027,1.9978,0.904,0.477,"negative regulation of signaling"),
c("GO:0035556","intracellular signal transduction",6.704,2.7959,0.774,0.505,"negative regulation of signaling"),
c("GO:0051051","negative regulation of transport",0.706,2.5157,0.809,0.512,"negative regulation of signaling"),
c("GO:1902306","negative regulation of sodium ion transmembrane transport",0.002,1.9245,0.821,0.523,"negative regulation of signaling"),
c("GO:0010646","regulation of cell communication",6.570,1.6784,0.818,0.529,"negative regulation of signaling"),
c("GO:0023051","regulation of signaling",6.570,1.6849,0.879,0.534,"negative regulation of signaling"),
c("GO:0008277","regulation of G-protein coupled receptor protein signaling pathway",0.358,1.7011,0.810,0.538,"negative regulation of signaling"),
c("GO:1901017","negative regulation of potassium ion transmembrane transporter activity",0.013,1.9245,0.797,0.575,"negative regulation of signaling"),
c("GO:0010648","negative regulation of cell communication",2.203,2.6180,0.798,0.588,"negative regulation of signaling"),
c("GO:0048585","negative regulation of response to stimulus",2.501,2.1675,0.863,0.598,"negative regulation of signaling"),
c("GO:0007165","signal transduction",16.054,2.3706,0.751,0.640,"negative regulation of signaling"),
c("GO:0051270","regulation of cellular component movement",1.289,1.7462,0.745,0.646,"negative regulation of signaling"),
c("GO:0009968","negative regulation of signal transduction",2.090,2.3449,0.759,0.662,"negative regulation of signaling"),
c("GO:0007166","cell surface receptor signaling pathway",8.919,1.9876,0.767,0.683,"negative regulation of signaling"),
c("GO:0055078","sodium ion homeostasis",0.081,2.0670,0.898,0.060,"sodium ion homeostasis"),
c("GO:0010817","regulation of hormone levels",1.029,2.0066,0.892,0.414,"sodium ion homeostasis"),
c("GO:0090066","regulation of anatomical structure size",0.957,1.7036,0.892,0.525,"sodium ion homeostasis"),
c("GO:0030644","cellular chloride ion homeostasis",0.015,1.6260,0.871,0.526,"sodium ion homeostasis"),
c("GO:0055081","anion homeostasis",0.072,1.6770,0.900,0.584,"sodium ion homeostasis"),
c("GO:0002268","follicular dendritic cell differentiation",0.005,1.6260,0.908,0.065,"follicular dendritic cell differentiation"),
c("GO:0002266","follicular dendritic cell activation",0.005,1.6260,0.944,0.383,"follicular dendritic cell differentiation"),
c("GO:0006790","sulfur compound metabolic process",0.742,3.0132,0.925,0.077,"sulfur compound metabolism"),
c("GO:0009812","flavonoid metabolic process",0.019,2.5467,0.958,0.081,"flavonoid metabolism"),
c("GO:1901616","organic hydroxy compound catabolic process",0.134,2.9431,0.911,0.096,"organic hydroxy compound catabolism"),
c("GO:0046185","aldehyde catabolic process",0.026,2.6904,0.879,0.326,"organic hydroxy compound catabolism"),
c("GO:0044282","small molecule catabolic process",0.575,1.7124,0.874,0.407,"organic hydroxy compound catabolism"),
c("GO:0046164","alcohol catabolic process",0.103,2.1605,0.865,0.659,"organic hydroxy compound catabolism"),
c("GO:0006584","catecholamine metabolic process",0.123,1.6345,0.894,0.668,"organic hydroxy compound catabolism"));
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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