Ilya 12/7/2018
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## Attaching package: 'reshape2'
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## corrplot 0.84 loaded
read in data from Brbic et al. (ProTraits: http://protraits.irb.hr/data.html)
PT = fread("ProTraits_precisionScores.txt",blank.lines.skip=TRUE)
# PT[1,]
names(PT)## [1] "Tax_ID" "Organism_name"
## [3] "Phenotype" "Minority"
## [5] "Original_label" "Hamap_+"
## [7] "Hamap_-" "MicrobeWiki_+"
## [9] "MicrobeWiki_-" "Wikipedia_+"
## [11] "Wikipedia_-" "Other_text_+"
## [13] "Other_text_-" "PMC_articles_+"
## [15] "PMC_articles_-" "Pubmed_abstracts_+"
## [17] "Pubmed_abstracts_-" "Proteome_composition_+"
## [19] "Proteome_composition_-" "Phyletic_profiles_+"
## [21] "Phyletic_profiles_-" "Coexisting_microbes_+"
## [23] "Coexisting_microbes_-" "Gene_neighbourhood_+"
## [25] "Gene_neighbourhood_-" "Codon_usage_bias_+"
## [27] "Codon_usage_bias_-" "Integrated_score_+"
## [29] "Integrated_score_-"
unique(PT$Phenotype)## [1] "alkaline_phosphatase"
## [2] "arbutin"
## [3] "cellobiose"
## [4] "d-arabinose"
## [5] "d-galacturonate"
## [6] "d-glucuronate"
## [7] "d-malic_acid"
## [8] "d-xylose"
## [9] "esterase_lipase__c8"
## [10] "esterase__c4"
## [11] "fructose"
## [12] "g-amino-butyric_acid"
## [13] "gelatin_hydrolysis"
## [14] "glutamate"
## [15] "glycerol"
## [16] "glycogen"
## [17] "hydrogen_sulfide"
## [18] "lactate"
## [19] "lactose"
## [20] "mannitol"
## [21] "melibiose"
## [22] "n-acetyl-neuraminic_acid"
## [23] "n-acetylglucosamine"
## [24] "quinic_acid"
## [25] "sorbitol"
## [26] "starch"
## [27] "sucrose"
## [28] "beta-glucosidase"
## [29] "catalase"
## [30] "d-arabitol"
## [31] "dextrin"
## [32] "formate"
## [33] "inosine"
## [34] "malate"
## [35] "raffinose"
## [36] "trehalose"
## [37] "urease"
## [38] "alpha-glucosidase"
## [39] "alpha-ketoglutaric_acid"
## [40] "alanine"
## [41] "d-saccharate"
## [42] "gentiobiose"
## [43] "gluconate"
## [44] "l-arabinose"
## [45] "l-rhamnose"
## [46] "nitrate_reduction"
## [47] "salicin"
## [48] "acetate"
## [49] "maltose"
## [50] "propionate"
## [51] "cystine_arylamidase"
## [52] "indole_production"
## [53] "lipase__c14"
## [54] "myo-inositol"
## [55] "n-acetyl-b-d-mannosamine"
## [56] "turanose"
## [57] "valine_arylamidase"
## [58] "beta-galactosidase"
## [59] "2-ketogluconate"
## [60] "adipate"
## [61] "aesculin"
## [62] "amygdalin"
## [63] "arginine_dihydrolase"
## [64] "aspartate"
## [65] "benzoate"
## [66] "casein"
## [67] "chymotrypsin"
## [68] "citrate"
## [69] "d-aspartic_acid"
## [70] "d-lyxose"
## [71] "ethanol"
## [72] "fructose-6-phosphate"
## [73] "glucose-6-phosphate"
## [74] "glucose"
## [75] "glycine"
## [76] "hippurate"
## [77] "histidine"
## [78] "l-arabitol"
## [79] "l-arginine"
## [80] "l-pyroglutamic_acid"
## [81] "l-sorbose"
## [82] "leucine"
## [83] "mannose"
## [84] "methyl_beta-d-glucopyranoside"
## [85] "methyl_beta-d-xylopyranoside"
## [86] "mucic_acid"
## [87] "n-acetyl-beta-glucosaminidase"
## [88] "oxidase"
## [89] "phenylacetate"
## [90] "serine"
## [91] "tagatose"
## [92] "trypsin"
## [93] "alpha-fucosidase"
## [94] "alpha-galactosidase"
## [95] "alpha-hydroxybutyric_acid"
## [96] "galactose"
## [97] "l-fucose"
## [98] "melezitose"
## [99] "naphthol-as-bi-phosphohydrolase"
## [100] "pyruvate"
## [101] "ribose"
## [102] "stachyose"
## [103] "voges–proskauer_reaction"
## [104] "alpha-mannosidase"
## [105] "d-fucose"
## [106] "beta-glucuronidase"
## [107] "inositol"
## [108] "malonate"
## [109] "tween_20_or_40"
## [110] "ecosystem=environmental"
## [111] "ecosystem=hostassociated"
## [112] "ecosystemcategory=animal"
## [113] "ecosystemcategory=aquatic"
## [114] "ecosystemcategory=biotransformation"
## [115] "ecosystemcategory=fish"
## [116] "ecosystemcategory=foodproduction"
## [117] "ecosystemcategory=human"
## [118] "ecosystemcategory=insecta"
## [119] "ecosystemcategory=mammals"
## [120] "ecosystemcategory=plants"
## [121] "ecosystemcategory=solidwaste"
## [122] "ecosystemcategory=terrestrial"
## [123] "ecosystemsubtype=blood"
## [124] "ecosystemsubtype=cerebrospinalfluid"
## [125] "ecosystemsubtype=fecal"
## [126] "ecosystemsubtype=foregut"
## [127] "ecosystemsubtype=hydrothermalvents"
## [128] "ecosystemsubtype=largeintestine"
## [129] "ecosystemsubtype=lentic"
## [130] "ecosystemsubtype=lotic"
## [131] "ecosystemsubtype=oceanic"
## [132] "ecosystemsubtype=oral"
## [133] "ecosystemsubtype=petrochemical"
## [134] "ecosystemsubtype=saltcrystallizerponds"
## [135] "ecosystemsubtype=wetlands"
## [136] "ecosystemtype=agriculturalfield"
## [137] "ecosystemtype=composting"
## [138] "ecosystemtype=digestivesystem"
## [139] "ecosystemtype=industrialwastewater"
## [140] "ecosystemtype=marine"
## [141] "ecosystemtype=phylloplane"
## [142] "ecosystemtype=reproductivesystem"
## [143] "ecosystemtype=respiratorysystem"
## [144] "ecosystemtype=rhizoplane"
## [145] "ecosystemtype=soil"
## [146] "ecosystemtype=thermalsprings"
## [147] "knownhabitats=aquatic"
## [148] "knownhabitats=biofilm"
## [149] "knownhabitats=creosotecontaminatedsoil"
## [150] "knownhabitats=deepsea"
## [151] "knownhabitats=feces"
## [152] "knownhabitats=freshwater"
## [153] "knownhabitats=gastrointestinaltract"
## [154] "knownhabitats=host"
## [155] "knownhabitats=hotspring"
## [156] "knownhabitats=humanoralcavity"
## [157] "knownhabitats=insectendosymbiont"
## [158] "knownhabitats=intestinaltract"
## [159] "knownhabitats=marine"
## [160] "knownhabitats=rhizosphere"
## [161] "knownhabitats=sediment"
## [162] "knownhabitats=sludge"
## [163] "knownhabitats=soil"
## [164] "knownhabitats=wastewater"
## [165] "phenotypes=acidophile"
## [166] "phenotypes=alkaliphile"
## [167] "specificecosystem=fecal"
## [168] "specificecosystem=rumen"
## [169] "specificecosystem=sediment"
## [170] "specificecosystem=sputum"
## [171] "ecosystemcategory=wastewater"
## [172] "ecosystemsubtype=intertidalzone"
## [173] "ecosystemtype=dairyproducts"
## [174] "knownhabitats=food"
## [175] "knownhabitats=humanairways"
## [176] "knownhabitats=hydrothermalvent"
## [177] "knownhabitats=plantroot"
## [178] "knownhabitats=rootnodule"
## [179] "ecosystemcategory=birds"
## [180] "ecosystemsubtype=vagina"
## [181] "ecosystemtype=circulatorysystem"
## [182] "knownhabitats=mud"
## [183] "ecosystemsubtype=nasopharyngeal"
## [184] "knownhabitats=endosymbiont"
## [185] "knownhabitats=oralcavity"
## [186] "ecosystemsubtype=urethra"
## [187] "ecosystemtype=freshwater"
## [188] "ecosystemtype=skin"
## [189] "knownhabitats=birdsintestinalmicroflora"
## [190] "knownhabitats=seawater"
## [191] "specificecosystem=urine"
## [192] "knownhabitats=humanintestinalmicroflora"
## [193] "knownhabitats=oilfields"
## [194] "knownhabitats=plantsymbiont"
## [195] "knownhabitats=skin"
## [196] "ecosystemcategory=bioremediation"
## [197] "ecosystemsubtype=mine"
## [198] "ecosystemsubtype=ponds"
## [199] "ecosystemtype=geologic"
## [200] "ecosystemtype=metal"
## [201] "ecosystemtype=nonmarinesalineandalkaline"
## [202] "knownhabitats=animalgastrointestinaltract"
## [203] "knownhabitats=compost"
## [204] "knownhabitats=gingivalcrevices"
## [205] "knownhabitats=humanvaginalmicroflora"
## [206] "knownhabitats=pig"
## [207] "knownhabitats=plants"
## [208] "knownhabitats=bovinerumen"
## [209] "knownhabitats=bovine"
## [210] "knownhabitats=surfacewater"
## [211] "knownhabitats=humanfecal"
## [212] "knownhabitats=humanskin"
## [213] "bioticrelationship=symbiotic"
## [214] "cellarrangement=chains"
## [215] "cellarrangement=clusters"
## [216] "cellarrangement=filaments"
## [217] "cellarrangement=pairs"
## [218] "cellarrangement=singles"
## [219] "energysource=autotroph"
## [220] "energysource=chemoorganotroph"
## [221] "energysource=heterotroph"
## [222] "energysource=lithotroph"
## [223] "energysource=methylotroph"
## [224] "energysource=photoautotroph"
## [225] "energysource=photosynthetic"
## [226] "energysource=phototroph"
## [227] "flagellarpresence"
## [228] "gram_stain=positive"
## [229] "growth_in_groups"
## [230] "habitat=aquatic"
## [231] "habitat=freeliving"
## [232] "habitat=hostassociated"
## [233] "habitat=single"
## [234] "habitat=terrestrial"
## [235] "halophilic"
## [236] "host=insectsgeneral"
## [237] "host=insectstermites"
## [238] "host=mammalscarnivora"
## [239] "host=mammalsherbivores"
## [240] "host=mammalsman"
## [241] "host=mammalspig"
## [242] "host=marineinvertebrates"
## [243] "host=plantsexceptlegumes"
## [244] "host=plantslegumes"
## [245] "host=ticks"
## [246] "mammalian_pathogen=enteric"
## [247] "mammalian_pathogen=nervous_system"
## [248] "mammalian_pathogen=oportunisticnosocomial"
## [249] "mammalian_pathogen=oral_cavity"
## [250] "mammalian_pathogen=respiratory_lungdisease"
## [251] "mammalian_pathogen=respiratory"
## [252] "mammalian_pathogen=respiratory_throatnoseeyes"
## [253] "mammalian_pathogen=urogenital"
## [254] "mammalian_pathogen=urogenital_reproductive"
## [255] "mammalian_pathogen=urogenital_urinary"
## [256] "metabolism=biomassdegrader"
## [257] "metabolism=cellulosedegrader"
## [258] "metabolism=ethanolproduction"
## [259] "metabolism=hydrogensulfidegasrelease"
## [260] "metabolism=ironoxidizer"
## [261] "metabolism=ironreducer"
## [262] "metabolism=methanogen"
## [263] "metabolism=nitrifying"
## [264] "metabolism=nitrogenfixation"
## [265] "metabolism=nitrogenproducer"
## [266] "metabolism=pahdegrading"
## [267] "metabolism=sulfatereducer"
## [268] "metabolism=sulfuroxidizer"
## [269] "mobility"
## [270] "motility"
## [271] "oxygenreq=facultative"
## [272] "oxygenreq=strictaero"
## [273] "oxygenreq=strictanaero"
## [274] "pathogenic_in_mammals"
## [275] "pathogenic_in_plants"
## [276] "radioresistance"
## [277] "shape=bacilli"
## [278] "shape=coccus"
## [279] "shape=filamentous"
## [280] "shape=spirilla"
## [281] "shape=tailed"
## [282] "sporulation"
## [283] "temperaturerange=hyperthermophilic"
## [284] "temperaturerange=mesophilic"
## [285] "temperaturerange=thermophilic"
## [286] "habitat=multiple"
## [287] "oxygenreq=microaerophilic"
## [288] "temperaturerange=psychrophilic"
## [289] "cellarrangement=tetrads"
## [290] "habitat=specialized"
## [291] "energysource=chemoautotroph"
## [292] "energysource=chemolithotroph"
## [293] "mammalian_pathogen=bone"
## [294] "energysource=chemoheterotroph"
## [295] "energysource=chemolithoautotroph"
## [296] "host=fish"
## [297] "mammalian_pathogen=cardiovascular"
## [298] "metabolism=sulfurrespiration"
## [299] "habitat=aquatic_salinewater"
## [300] "metabolism=ammoniaoxidizer"
## [301] "metabolism=storespolyhydroxybutyrate"
## [302] "pathogenic_in_fish"
## [303] "energysource=oligotroph"
## [304] "metabolism=acetogen"
## [305] "mammalian_pathogen=cardiovascular_blood"
## [306] "mammalian_pathogen=skin_softtissues"
## [307] "mammalian_pathogen=softtissues"
## [308] "(secondari,metabolit,mycelium,antibiot,spore)"
## [309] "(rumen,bovin,rumin,cattl,degrad)"
## [310] "(australia,infecti,queensland,fill,fluid)"
## [311] "(vaccin,immun,antibodi,infect,protect)"
## [312] "(ethanol,ferment,acet,succin,lactat)"
## [313] "(aerial,mycelium,spore,hypha,soil)"
## [314] "(symbiosi,replicon,nitrogen,nitrogenfix,streptomycinresist)"
## [315] "(prophag,instanc,variat,diverg,newli)"
## [316] "(bacteriochlorophyl,photosystem,photosynthesi,chlorophyl,oxygen)"
## [317] "(spring,mat,hot,yellowston,moder)"
## [318] "(sauc,lactic,soi,salt,ferment)"
## [319] "(vertic,alkaliphil,bacteriom,sharpshoot,agreement)"
## [320] "(sporeform,gramposit,nonmotil,motil,rodshap)"
## [321] "(benzen,toluen,degrad,aromat,hydrocarbon)"
## [322] "(blight,fire,shoot,pathogen,japan)"
## [323] "(pyren,pah,naphthalen,polycycl,anthracen)"
## [324] "(brucellosi,infect,transmit,vaccin,pathogen)"
## [325] "(buruli,chancroid,ulcer,mycolacton,endem)"
## [326] "(ocean,coastal,plankton,inorgan,suspend)"
## [327] "(unicellular,photosystem,photosynthesi,ocean,fixat)"
## [328] "(subsurfac,sulfatereduc,piezophil,aquif,groundwat)"
## [329] "(sludg,wastewat,reactor,bioreactor,kei)"
## [330] "(fe,anod,mfc,electrod,electr)"
## [331] "(staphylococci,staphylococc,methicillin,urinari,coagulaseneg)"
## [332] "(nitrogenfix,symbiosi,fixat,rhizospher,rhizobia)"
## [333] "(tickborn,pathogen,virul,rickettsiosi,infect)"
## [334] "(cystic,fibrosi,patient,lung,infect)"
## [335] "(radiat,ioniz,usa,desicc,repair)"
## [336] "(gastric,gastriti,spiralshap,biopsi,microaerophil)"
## [337] "(methylotroph,methanol,formaldehyd,pinkpig,methylamin)"
## [338] "(rot,crop,econom,phytopathogen,unclear)"
## [339] "(alkaliphil,sodiumdepend,halotoler,proton,transloc)"
## [340] "(phosphoru,ebpr,wastewat,polyphosph,treatment)"
## [341] "(flora,vagin,tract,vaginosi,reproduct)"
## [342] "(virul,island,capsul,invas,transport)"
## [343] "(borreliosi,infect,pathogen,tickborn,antigen)"
## [344] "(pha,polyhydroxyalkano,phb,accumul,carbon)"
## [345] "(salin,optimum,hypersalin,salt,oil)"
## [346] "(deepsea,piezophil,pressur,depth,hydrostat)"
## [347] "(toxin,crystal,insecticid,gut,spore)"
## [348] "(glide,motil,motor,pigment,pathogen)"
## [349] "(nitrogenfix,symbiosi,fixat,toluen,protect)"
## [350] "(permafrost,siberian,psychrophil,cold,antarct)"
## [351] "(haloarchaea,hypersalin,archaeal,seafood,nacl)"
## [352] "(paddi,anox,bog,toluen,divers)"
## [353] "(tetanu,toxin,spore,botul,toxoid)"
## [354] "(ehrlichiosi,monocyt,granulocyt,macrophag,anaplasmosi)"
## [355] "(prei,predatori,predat,attack,flagellum)"
## [356] "(tooth,dental,cari,caviti,plaqu)"
## [357] "(uranium,bioremedi,subsurfac,remedi,contamin)"
## [358] "(blackleg,rot,stem,unclear,pathogen)"
## [359] "(bioaugment,wastewat,wast,degrad,biodegrad)"
## [360] "(nitrit,ammoniaoxid,nitrif,ammonium,nitrat)"
## [361] "(cytochrom,fe,heme,ctype,dissimilatori)"
## [362] "(gut,diet,glycan,obes,reduc)"
## [363] "(fe,acceptor,dissimilatori,metal,donor)"
## [364] "(magnetosom,magnetit,amb1,magnetotaxi,crystal)"
## [365] "(hyperthermophil,archaeal,hydrotherm,vent,heterotroph)"
## [366] "(dehalogen,ethen,dehalogenas,dechlorin,halogen)"
## [367] "(kimchi,ferment,korean,ingredi,season)"
## [368] "(sheath,south,coast,korea,hole)"
## [369] "(vent,hydrotherm,deepsea,chemolithoautotroph,sulfuroxid)"
## [370] "(syntroph,acetateoxid,acet,isobutyr,fatti)"
## [371] "(lous,nymph,relaps,patient,adult)"
## [372] "(infect,patient,pathogen,virul,opportunist)"
## [373] "(thermophil,spring,hot,cellulolyt,optimum)"
## [374] "(spore,crystal,sporul,toxic,polysaccharid)"
## [375] "(legum,symbiosi,rhizobia,nod,stem)"
## [376] "(alkan,oil,crude,hydrocarbon,degrad)"
## [377] "(sulfatereduc,sulfat,dissimilatori,sulfit,acceptor)"
## [378] "(methan,methanogenesi,acet,methanol,dioxid)"
## [379] "(lactic,chees,food,ferment,milk)"
## [380] "(meat,raw,ferment,fresh,food)"
## [381] "(heterocyst,fixat,veget,aquat,carbon)"
## [382] "(japan,paddi,anox,gramneg,rod)"
## [383] "(denitrif,nitrat,nitrit,reductas,nitrou)"
## [384] "(cellulos,cellulosom,cellulolyt,xylan,cellulas)"
## [385] "(hypha,gramposit,aerial,antibiot,spore)"
## [386] "(nonpathogen,blight,fire,shoot,motil)"
## [387] "(virul,pathogen,highli,econom,motil)"
## [388] "(spring,hot,arsen,optim,arsenit)"
## [389] "(periodont,gingiv,bone,dental,plaqu)"
## [390] "(relaps,tickborn,lous,transmit,epidem)"
## [391] "(anox,sediment,ground,nonmotil,reclassifi)"
## [392] "(acidophil,thermophil,thermoacidophil,heterotroph,dissimilatori)"
## [393] "(nocardiosi,subord,pulmonari,immunocompromis,chronic)"
## [394] "(acidophil,thermophil,pyrit,bioleach,drainag)"
## [395] "(leprosi,india,brazil,nerv,patient)"
## [396] "(fungal,antifung,phenazin,biocontrol,rot)"
## [397] "(beer,spoilag,spoil,lactic,beverag)"
## [398] "(faec,nonsporeform,nonmotil,gramneg,rodshap)"
## [399] "(psychrophil,cold,sediment,inhabit,irregular)"
## [400] "(goat,mastiti,mycoplasm,polyarthr,cow)"
## [401] "(soybean,legum,max,rhizobia,fastgrow)"
## [402] "(autotroph,replic,fixat,metabol,aggreg)"
## [403] "(smallest,intein,extrachromosom,freeliv,ocean)"
## [404] "(symbiosi,island,nativ,australia,dispens)"
## [405] "(subord,stalk,mother,swarmer,averag)"
## [406] "(hydrogenotroph,nacl,optimum,sakai,moder)"
## [407] "(appendag,nearest,distinct,rich,resembl)"
## [408] "(ferment,spoilag,lactic,kimchi,korean)"
## [409] "(cem,mare,metriti,contagi,stallion)"
## [410] "(sulphur,acidophil,metal,reduc,fe)"
## [411] "(xylanas,xylan,cellulas,hydrolysi,flagellin)"
## [412] "(faec,sporeform,gramposit,rodshap,capabl)"
## [413] "(gramposit,motil,sporeform,whippl,multisystem)"
## [414] "(rhizospher,nitrogenfix,nitrogen,replicon,gramneg)"
## [415] "(ectoin,salin,salt,mutant,optimum)"
## [416] "(halotoler,salt,mesophil,pictur,iran)"
## [417] "(disproportion,mesophil,thiosulf,metabol,sulfatereduc)"
## [418] "(psychrotoler,nearest,flat,glucos,chlorid)"
## [419] "knownhabitats=urogenitaltract"
## [420] "ecosystemsubtype=alkaline"
## [421] "mammalian_pathogen=cardiovascular_heart_bloodvessels"
## [422] "metabolism=carbondioxidefixation"
## [423] "(bioluminesc,gramneg,nonmotil,reliabl,biodegrad)"
## [424] "(subsurfac,geochem,deep,aquif,depth)"
# PT_wide = reshape(PT, idvar = "Organism_name", timevar = "Phenotype", direction = "wide")
PT$Organism_name=factor(PT$Organism_name)
PT$Phenotype=factor(PT$Phenotype)
PT$`Integrated_score_+`=as.numeric(PT$`Integrated_score_+`)## Warning: NAs introduced by coercion
dfmatrix <- acast(PT, Organism_name ~ Phenotype,value.var='Integrated_score_+',fun.aggregate=sum,margins=FALSE)
corrmatrix <- cor(dfmatrix, use="pairwise")## Warning in cor(dfmatrix, use = "pairwise"): the standard deviation is zero
col1 <- colorRampPalette(brewer.pal(9,"BrBG"))
corrplot(corrmatrix, method = "color", type = "upper",
cl.pos = "n", tl.pos = "n")
read in data from Barberan et al. 2016 (IJSEM: https://figshare.com/articles/International_Journal_of_Systematic_and_Evolutionary_Microbiology_IJSEM_phenotypic_database/4272392)
path = "4272392/"
#read table
ijsem<-read.delim(paste0(path,"IJSEM_pheno_db_v1.0.txt"), sep="\t", header=T, check.names=F, fill=T,
na.strings=c("NA", "", "Not indicated", " Not indicated","not indicated", "Not Indicated", "n/a", "N/A", "Na", "Not given", "not given","Not given for yeasts", "not indicated, available in the online version", "Not indicated for yeasts", "Not Stated", "Not described for yeasts", "Not determined", "Not determined for yeasts"))
#simplify column names
colnames(ijsem)<-c("Habitat", "Year", "DOI", "rRNA16S", "GC", "Oxygen",
"Length", "Width", "Motility", "Spore", "MetabAssays", "Genus", "Species", "Strain", "pH_optimum", "pH_range", "Temp_optimum", "Temp_range", "Salt_optimum", "Salt_range", "Pigment", "Shape", "Aggregation", "FirstPage", "CultureCollection", "CarbonSubstrate", "Genome", "Gram", "Subhabitat", "Biolog")
#clean Habitat column
levels(ijsem$Habitat)[levels(ijsem$Habitat)=="freshwater (river, lake, pond)"]<-"freshwater"
levels(ijsem$Habitat)[levels(ijsem$Habitat)=="freshwater sediment (river, lake, pond"]<-"freshwater sediment"
#clean Oxygen column
levels(ijsem$Oxygen)[levels(ijsem$Oxygen)=="aerobic"]<-"obligate aerobe"
levels(ijsem$Oxygen)[levels(ijsem$Oxygen)=="anerobic"]<-"obligate anerobe"
levels(ijsem$Oxygen)[levels(ijsem$Oxygen)=="microerophile"]<-"microaerophile"
#clean pH_optimum column
ijsem$pH_optimum<-as.character(ijsem$pH_optimum)
#this step splits the range values and takes the mean value
#values that are not numeric are transformed to NAs
ijsem$pH_optimum<-suppressWarnings(sapply(ijsem$pH_optimum, simplify=T, function(x){mean(as.numeric(unlist(strsplit(x, split="-", fixed=T))))}))
#remove pH values <0 and >10
ijsem$pH_optimum[ijsem$pH_optimum<0 | ijsem$pH_optimum>10]<-NA
#clean Temp_optimum column
ijsem$Temp_optimum<-as.character(ijsem$Temp_optimum)
#this step splits the range values and takes the mean value
#values that are not numeric are transformed to NAs
ijsem$Temp_optimum<-suppressWarnings(sapply(ijsem$Temp_optimum, simplify=T, function(x){mean(as.numeric(unlist(strsplit(x, split="-", fixed=T))))}))
#clean Salt_optimum column
ijsem$Salt_optimum<-as.character(ijsem$Salt_optimum)
#this step splits the range values and takes the mean value
#values that are not numeric are transformed to NAs
ijsem$Salt_optimum<-suppressWarnings(sapply(ijsem$Salt_optimum, simplify=T, function(x){mean(as.numeric(unlist(strsplit(x, split="-", fixed=T))))}))
#there are some formatting issues that should be solved
summary(ijsem)## Habitat Year DOI
## other :1853 Min. :2004 10.1099/ijs.0.054098-0: 27
## soil :1089 1st Qu.:2007 10.1099/ijs.0.051540-0: 26
## seawater : 401 Median :2009 10.1099/ijs.0.051045-0: 25
## marine sediment : 329 Mean :2009 10.1099/ijs.0.053306-0: 20
## plant associated: 297 3rd Qu.:2012 10.1099/ijs.0.63527-0 : 12
## (Other) :1139 Max. :2015 (Other) :5010
## NA's : 20 NA's : 8
## rRNA16S GC Oxygen
## JN565849 : 28 72 : 48 obligate aerobe :3206
## HG1315102: 25 67 : 42 anaerobic : 573
## JX402080 : 24 40.8 : 41 facultative aerobe : 86
## KC525204 : 23 68.5 : 40 facultative anaerobe: 617
## KC447383 : 9 71 : 35 microaerophile : 45
## (Other) :4940 (Other):4279 NA's : 601
## NA's : 79 NA's : 643
## Length Width Motility
## 2 : 165 0.5 : 348 axial filament : 9
## 2.5 : 155 0.6 : 199 flagella :1157
## 1.5 : 136 0.7 : 173 gliding : 166
## 3 : 109 0.75 : 173 motile, but unspecified structure: 707
## 1.75 : 94 0.4 : 172 non-motile :2384
## (Other):3150 (Other):2852 NA's : 705
## NA's :1319 NA's :1211
## Spore
## no :2423
## yes :1028
## NA's:1677
##
##
##
##
## MetabAssays
## catalase positive, oxidase positive : 369
## catalase positive : 244
## catalase positive, nitrate reduction to nitrite, oxidase positive: 173
## aesculin hydrolysis : 118
## aesculin hydrolysis, catalase positive, oxidase positive : 106
## (Other) :3345
## NA's : 773
## Genus Species Strain
## Bacillus : 119 soli : 57 7747T : 26
## Streptomyces : 106 marina : 38 49061T : 25
## Paenibacillus : 78 xinjiangensis: 35 YDT : 25
## Flavobacterium: 74 ginsengisoli : 32 J4T : 18
## Lactobacillus : 72 marinus : 31 J4 : 6
## Mycobacterium : 68 koreensis : 30 (Other):5020
## (Other) :4611 (Other) :4905 NA's : 8
## pH_optimum pH_range Temp_optimum Temp_range
## Min. : 0.750 06-Sep : 216 Min. : 3.0 Oct-37 : 210
## 1st Qu.: 7.000 06-Aug : 189 1st Qu.: 27.5 15-37 : 191
## Median : 7.000 7 : 167 Median : 30.0 Oct-40 : 158
## Mean : 7.208 05-Sep : 152 Mean : 31.4 Apr-37 : 154
## 3rd Qu.: 7.500 05-Oct : 143 3rd Qu.: 34.0 20-37 : 143
## Max. :10.000 (Other):2974 Max. :300.0 (Other):3754
## NA's :1634 NA's :1287 NA's :764 NA's : 518
## Salt_optimum Salt_range Pigment Shape
## Min. : 0.000 0 : 230 no : 721 cocci : 464
## 1st Qu.: 0.500 0-2 : 183 yes :3118 ovoid/coccobacillus: 376
## Median : 2.000 0-1 : 182 NA's:1289 rod :3773
## Mean : 3.238 0-3 : 172 spirillum/corkscrew: 48
## 3rd Qu.: 3.500 0-5 : 150 NA's : 467
## Max. :232.000 (Other):2937
## NA's :2387 NA's :1274
## Aggregation FirstPage CultureCollection
## chain:1135 60 : 40 CECT8312T|DSM27088T : 17
## clump: 670 33 : 34 DSM25287T|NCCB100398T : 15
## none : 204 39 : 33 JCM18565T|KCTC29126T : 15
## NA's :3119 27 : 28 CGMCC1.12331T|JCM18732T : 12
## 1471 : 13 ATCCBAA-1391T|VKMB-2447T: 3
## (Other):4979 (Other) :5049
## NA's : 1 NA's : 17
## CarbonSubstrate
## Tween 80 : 29
## glucose : 26
## fructose, galactose, lactose, maltose, mannose, raffinose, sucrose : 19
## acetate, butanol, ethanol, fructose, galactose, glucosamine, glucose, glycerol, lactate, maltose, melibiose, propionic acid (propionate), pyruvic acid (pyruvate), raffinose, succinic acid (succinate), sucrose, valerate: 18
## acetate : 16
## (Other) :4570
## NA's : 450
## Genome Gram
## CAUK01000001\xe4\xf3\xf1 CAUK01000006: 15 negative:2871
## CAUK01000001\xe4\xf3\xf1CAUK01000006 : 3 positive:1846
## CAUK01000001-CAUK01000006 : 2 variable: 85
## AB208062 : 1 NA's : 326
## CAUJ01000001\xe4\xf3\xf1CAUJ01000008: 1
## (Other) : 67
## NA's :5039
## Subhabitat Biolog
## air sample : 24 No :3811
## tidal flat sediment: 22 Yes :1316
## Sludge : 18 Yes, No: 1
## salt lake : 17
## marine sponge : 16
## (Other) :1868
## NA's :3163