setwd('/Users/emmatimminsschiffman/Documents/Dissertation/dissertation drafts/images for prezi') # 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 , 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:0006006","glucose metabolic process",1.142,10.2798,0.873,0.000,"glucose metabolism"), c("GO:0016052","carbohydrate catabolic process",1.307,5.0857,0.864,0.586,"glucose metabolism"), c("GO:0044275","cellular carbohydrate catabolic process",0.178,7.1325,0.850,0.604,"glucose metabolism"), c("GO:0005977","glycogen metabolic process",0.133,2.2693,0.829,0.635,"glucose metabolism"), c("GO:0006800","oxygen and reactive oxygen species metabolic process",0.172,1.4660,0.992,0.000,"oxygen and reactive oxygen species metabolism"), c("GO:0007010","cytoskeleton organization",0.232,11.6517,0.653,0.000,"cytoskeleton organization"), c("GO:0032271","regulation of protein polymerization",0.030,5.7645,0.684,0.429,"cytoskeleton organization"), c("GO:0006323","DNA packaging",0.289,1.4721,0.638,0.591,"cytoskeleton organization"), c("GO:0000305","response to oxygen radical",0.000,1.2714,0.954,0.613,"cytoskeleton organization"), c("GO:0003006","developmental process involved in reproduction",0.106,1.3626,0.832,0.553,"cytoskeleton organization"), c("GO:0006818","hydrogen transport",0.884,2.7486,0.833,0.400,"cytoskeleton organization"), c("GO:0051235","maintenance of location",0.034,2.0559,0.856,0.545,"cytoskeleton organization"), c("GO:0016044","cellular membrane organization",0.245,1.2654,0.700,0.656,"cytoskeleton organization"), c("GO:0021700","developmental maturation",0.031,1.1148,0.789,0.547,"cytoskeleton organization"), c("GO:0016337","cell-cell adhesion",0.088,1.2908,0.844,0.625,"cytoskeleton organization"), c("GO:0030721","spectrosome organization",0.000,2.0520,0.778,0.435,"cytoskeleton organization"), c("GO:0007294","germarium-derived oocyte fate determination",0.000,3.1864,0.726,0.134,"cytoskeleton organization"), c("GO:0048610","cellular process involved in reproduction",0.597,1.4523,0.903,0.510,"cytoskeleton organization"), c("GO:0006890","retrograde vesicle-mediated transport, Golgi to ER",0.007,1.4951,0.829,0.508,"cytoskeleton organization"), c("GO:0007265","Ras protein signal transduction",0.169,2.6557,0.767,0.606,"cytoskeleton organization"), c("GO:0070271","protein complex biogenesis",0.661,1.0762,0.778,0.568,"cytoskeleton organization"), c("GO:0007264","small GTPase mediated signal transduction",0.405,3.3019,0.754,0.308,"cytoskeleton organization"), c("GO:0019953","sexual reproduction",0.079,1.5435,0.932,0.320,"cytoskeleton organization"), c("GO:0010038","response to metal ion",0.103,1.0356,0.945,0.608,"cytoskeleton organization"), c("GO:0045995","regulation of embryonic development",0.013,1.2753,0.716,0.691,"cytoskeleton organization"), c("GO:0008637","apoptotic mitochondrial changes",0.007,1.3290,0.714,0.596,"cytoskeleton organization"), c("GO:0035317","imaginal disc-derived wing hair organization",0.001,1.6981,0.667,0.570,"cytoskeleton organization"), c("GO:0044087","regulation of cellular component biogenesis",0.142,3.9914,0.734,0.449,"cytoskeleton organization"), c("GO:0016192","vesicle-mediated transport",0.652,1.1679,0.952,0.325,"cytoskeleton organization"), c("GO:0045454","cell redox homeostasis",0.592,5.0867,0.738,0.226,"cytoskeleton organization"), c("GO:0010035","response to inorganic substance",0.221,2.3199,0.949,0.347,"cytoskeleton organization"), c("GO:0030865","cortical cytoskeleton organization",0.005,2.4892,0.694,0.598,"cytoskeleton organization"), c("GO:0045478","fusome organization",0.000,2.0520,0.765,0.468,"cytoskeleton organization"), c("GO:0015985","energy coupled proton transport, down electrochemical gradient",0.595,3.0915,0.798,0.242,"cytoskeleton organization"), c("GO:0060047","heart contraction",0.017,1.6981,0.790,0.524,"cytoskeleton organization"), c("GO:0008104","protein localization",1.977,1.7869,0.928,0.322,"cytoskeleton organization"), c("GO:0060711","labyrinthine layer development",0.005,1.4015,0.767,0.644,"cytoskeleton organization"), c("GO:0007155","cell adhesion",0.622,1.6206,0.823,0.243,"cytoskeleton organization"), c("GO:0002165","instar larval or pupal development",0.007,1.3760,0.772,0.694,"cytoskeleton organization"), c("GO:0032504","multicellular organism reproduction",0.084,1.2534,0.842,0.576,"cytoskeleton organization"), c("GO:0031034","myosin filament assembly",0.001,1.9553,0.688,0.532,"cytoskeleton organization"), c("GO:0031033","myosin filament organization",0.001,1.9553,0.709,0.567,"cytoskeleton organization"), c("GO:0043933","macromolecular complex subunit organization",1.196,2.8589,0.761,0.579,"cytoskeleton organization"), c("GO:0045103","intermediate filament-based process",0.003,1.1624,0.872,0.151,"cytoskeleton organization"), c("GO:0045104","intermediate filament cytoskeleton organization",0.003,1.2714,0.700,0.598,"cytoskeleton organization"), c("GO:0007566","embryo implantation",0.004,1.4951,0.747,0.619,"cytoskeleton organization"), c("GO:0001539","ciliary or flagellar motility",0.444,2.5042,0.812,0.276,"cytoskeleton organization"), c("GO:0009791","post-embryonic development",0.053,1.1678,0.750,0.631,"cytoskeleton organization"), c("GO:0007017","microtubule-based process",0.294,5.4437,0.835,0.208,"cytoskeleton organization"), c("GO:0007016","cytoskeletal anchoring at plasma membrane",0.003,2.5241,0.633,0.568,"cytoskeleton organization"), c("GO:0001763","morphogenesis of a branching structure",0.028,1.5036,0.761,0.544,"cytoskeleton organization"), c("GO:0048667","cell morphogenesis involved in neuron differentiation",0.053,1.3765,0.598,0.676,"cytoskeleton organization"), c("GO:0051591","response to cAMP",0.004,1.5911,0.950,0.694,"cytoskeleton organization"), c("GO:0006979","response to oxidative stress",0.274,1.3131,0.959,0.354,"cytoskeleton organization"), c("GO:0007517","muscle organ development",0.045,1.8117,0.731,0.429,"cytoskeleton organization"), c("GO:0007444","imaginal disc development",0.007,1.6491,0.767,0.653,"cytoskeleton organization"), c("GO:0051129","negative regulation of cellular component organization",0.071,1.5830,0.655,0.603,"cytoskeleton organization"), c("GO:0030029","actin filament-based process",0.123,7.4921,0.844,0.194,"cytoskeleton organization"), c("GO:0030030","cell projection organization",0.456,2.4575,0.692,0.619,"cytoskeleton organization"), c("GO:0034220","ion transmembrane transport",1.746,2.7158,0.787,0.631,"cytoskeleton organization"), c("GO:0034614","cellular response to reactive oxygen species",0.088,2.1264,0.799,0.601,"cytoskeleton organization"), c("GO:0006928","cellular component movement",0.674,1.5740,0.825,0.246,"cytoskeleton organization"), c("GO:0006911","phagocytosis, engulfment",0.004,1.8754,0.744,0.374,"cytoskeleton organization"), c("GO:0006901","vesicle coating",0.010,1.4081,0.687,0.619,"cytoskeleton organization"), c("GO:0048754","branching morphogenesis of an epithelial tube",0.022,1.3552,0.751,0.616,"cytoskeleton organization"), c("GO:0007626","locomotory behavior",0.022,1.5859,0.969,0.000,"locomotory behavior"), c("GO:0022610","biological adhesion",2.091,1.5544,0.993,0.000,"biological adhesion"), c("GO:0015980","energy derivation by oxidation of organic compounds",3.979,7.7721,0.873,0.022,"energy derivation by oxidation of organic compounds"), c("GO:0055114","oxidation-reduction process",16.017,3.5317,0.922,0.275,"energy derivation by oxidation of organic compounds"), c("GO:0043648","dicarboxylic acid metabolic process",1.097,1.2032,0.873,0.429,"energy derivation by oxidation of organic compounds"), c("GO:0009074","aromatic amino acid family catabolic process",0.045,1.5788,0.842,0.662,"energy derivation by oxidation of organic compounds"), c("GO:0010608","posttranscriptional regulation of gene expression",0.540,1.5996,0.835,0.354,"energy derivation by oxidation of organic compounds"), c("GO:0009109","coenzyme catabolic process",0.036,3.5331,0.889,0.493,"energy derivation by oxidation of organic compounds"), c("GO:0006732","coenzyme metabolic process",2.516,3.3116,0.904,0.642,"energy derivation by oxidation of organic compounds"), c("GO:0009205","purine ribonucleoside triphosphate metabolic process",4.744,4.6615,0.792,0.293,"energy derivation by oxidation of organic compounds"), c("GO:0006570","tyrosine metabolic process",0.048,1.8184,0.877,0.664,"energy derivation by oxidation of organic compounds"), c("GO:0006559","L-phenylalanine catabolic process",0.017,3.0255,0.849,0.623,"energy derivation by oxidation of organic compounds"), c("GO:0006558","L-phenylalanine metabolic process",0.058,2.8229,0.875,0.336,"energy derivation by oxidation of organic compounds"), c("GO:0006112","energy reserve metabolic process",0.134,2.2693,0.904,0.564,"energy derivation by oxidation of organic compounds"), c("GO:0006108","malate metabolic process",0.113,1.8184,0.894,0.354,"energy derivation by oxidation of organic compounds"), c("GO:0006099","tricarboxylic acid cycle",0.480,3.2418,0.887,0.648,"energy derivation by oxidation of organic compounds"), c("GO:0006090","pyruvate metabolic process",0.213,4.8013,0.889,0.206,"energy derivation by oxidation of organic compounds"), c("GO:0046164","alcohol catabolic process",0.099,6.6383,0.867,0.137,"energy derivation by oxidation of organic compounds"), c("GO:0006084","acetyl-CoA metabolic process",0.129,3.9626,0.883,0.300,"energy derivation by oxidation of organic compounds"), c("GO:0009894","regulation of catabolic process",0.220,1.6654,0.839,0.346,"energy derivation by oxidation of organic compounds"), c("GO:0051187","cofactor catabolic process",0.051,3.3990,0.891,0.466,"energy derivation by oxidation of organic compounds"), c("GO:0042743","hydrogen peroxide metabolic process",0.044,1.5772,0.959,0.044,"hydrogen peroxide metabolism"), c("GO:0008380","RNA splicing",0.164,8.7212,0.881,0.056,"RNA splicing"), c("GO:0032268","regulation of cellular protein metabolic process",0.675,1.6298,0.773,0.596,"RNA splicing"), c("GO:0016071","mRNA metabolic process",0.651,6.2111,0.881,0.292,"RNA splicing"), c("GO:0051340","regulation of ligase activity",0.004,1.9638,0.883,0.475,"RNA splicing"), c("GO:0043603","cellular amide metabolic process",0.824,1.1508,0.919,0.130,"RNA splicing"), c("GO:0045429","positive regulation of nitric oxide biosynthetic process",0.003,1.4015,0.850,0.508,"RNA splicing"), c("GO:0010498","proteasomal protein catabolic process",0.047,1.4353,0.857,0.671,"RNA splicing"), c("GO:0051443","positive regulation of ubiquitin-protein ligase activity",0.002,2.5042,0.793,0.276,"RNA splicing"), c("GO:0043433","negative regulation of sequence-specific DNA binding transcription factor activity",0.012,1.5911,0.800,0.489,"RNA splicing"), c("GO:0043392","negative regulation of DNA binding",0.031,1.2565,0.877,0.652,"RNA splicing"), c("GO:0051084","'de novo' posttranslational protein folding",0.016,1.4015,0.906,0.541,"RNA splicing"), c("GO:0006412","translation",5.031,4.3625,0.838,0.561,"RNA splicing"), c("GO:0006414","translational elongation",0.839,4.9747,0.861,0.455,"RNA splicing"), c("GO:0006396","RNA processing",2.803,1.7651,0.861,0.388,"RNA splicing"), c("GO:0006397","mRNA processing",0.542,7.1481,0.866,0.597,"RNA splicing"), c("GO:0006458","'de novo' protein folding",0.016,2.2993,0.906,0.322,"RNA splicing"), c("GO:0006457","protein folding",0.852,5.0560,0.881,0.148,"RNA splicing"), c("GO:0031145","anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process",0.006,1.9032,0.871,0.301,"RNA splicing"), c("GO:0009820","alkaloid metabolic process",0.003,2.0805,0.941,0.070,"alkaloid metabolism"), c("GO:0006749","glutathione metabolic process",0.128,1.8217,0.871,0.457,"alkaloid metabolism"), c("GO:0006769","nicotinamide metabolic process",0.000,2.1820,0.925,0.118,"alkaloid metabolism"), c("GO:0051186","cofactor metabolic process",3.252,1.9611,0.944,0.072,"cofactor metabolism"), c("GO:0006091","generation of precursor metabolites and energy",5.328,14.8447,0.941,0.078,"generation of precursor metabolites and energy")); 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()