count_words.RdCalculate word frequency
count_words(term,
exclude_words = NULL, stop_words = stopwords(),
min_word_length = 1, tokenizer = 'words', transform_case = tolower,
remove_numbers = TRUE, remove_punctuation = TRUE, custom_transformer = NULL,
stemming = FALSE, dictionary = NULL)A vector of description texts.
The words that should be excluded.
The stop words that should be be removed.
Minimum length of the word to be counted.
The tokenizer function, one of the values accepted by tm::termFreq.
The function normalizing lettercase of the words.
Whether to remove numbers.
Whether to remove punctuation.
Custom function that transforms words.
Whether to only keep the roots of inflected words.
A vector of words to be counted (if given all other words will be excluded).
The text preprocessing followings the instructions from http://www.sthda.com/english/wiki/word-cloud-generator-in-r-one-killer-function-to-do-everything-you-need .
A data frame with words and frequencies.
gm = readRDS(system.file("extdata", "random_GO_BP_sim_mat.rds", package = "simplifyEnrichment"))
go_id = rownames(gm)
go_term = AnnotationDbi::select(GO.db::GO.db, keys = go_id, columns = "TERM")$TERM
#> 'select()' returned 1:1 mapping between keys and columns
count_words(go_term)
#> word freq
#> regulation regulation 180
#> process process 63
#> positive positive 62
#> cell cell 59
#> negative negative 57
#> signaling signaling 44
#> pathway pathway 38
#> response response 36
#> development development 32
#> protein protein 32
#> transport transport 26
#> ion ion 22
#> metabolic metabolic 21
#> activity activity 20
#> receptor receptor 19
#> cellular cellular 18
#> assembly assembly 17
#> biosynthetic biosynthetic 17
#> catabolic catabolic 17
#> dna dna 17
#> morphogenesis morphogenesis 16
#> factor factor 15
#> differentiation differentiation 13
#> involved involved 12
#> calcium calcium 11
#> production production 11
#> transmembrane transmembrane 11
#> complex complex 10
#> apoptotic apoptotic 9
#> formation formation 9
#> growth growth 9
#> membrane membrane 9
#> migration migration 9
#> muscle muscle 9
#> adhesion adhesion 8
#> cardiac cardiac 8
#> homeostasis homeostasis 8
#> localization localization 8
#> organization organization 8
#> transcription transcription 8
#> acid acid 7
#> activation activation 7
#> cycle cycle 7
#> histone histone 7
#> mitochondrion mitochondrion 7
#> via via 7
#> import import 6
#> maintenance maintenance 6
#> mitochondrial mitochondrial 6
#> plasma plasma 6
#> proliferation proliferation 6
#> t t 6
#> endothelial endothelial 5
#> establishment establishment 5
#> methylation methylation 5
#> mrna mrna 5
#> neuron neuron 5
#> processing processing 5
#> rna rna 5
#> secretion secretion 5
#> stimulus stimulus 5
#> atp atp 4
#> blood blood 4
#> checkpoint checkpoint 4
#> chemokine chemokine 4
#> chromosome chromosome 4
#> damage damage 4
#> endosome endosome 4
#> fatty fatty 4
#> golgi golgi 4
#> immune immune 4
#> interleukinmediated interleukinmediated 4
#> lipoprotein lipoprotein 4
#> meiotic meiotic 4
#> metanephric metanephric 4
#> microtubule microtubule 4
#> mitotic mitotic 4
#> nuclear nuclear 4
#> oxygen oxygen 4
#> particle particle 4
#> polymerase polymerase 4
#> replication replication 4
#> smooth smooth 4
#> sodium sodium 4
#> transporter transporter 4
#> viral viral 4
#> virus virus 4
#> across across 3
#> actin actin 3
#> adaptive adaptive 3
#> adenylate adenylate 3
#> along along 3
#> atrial atrial 3
#> binding binding 3
#> body body 3
#> chemotaxis chemotaxis 3
#> cord cord 3
#> deubiquitination deubiquitination 3
#> division division 3
#> embryonic embryonic 3
#> epidermal epidermal 3
#> epithelial epithelial 3
#> export export 3
#> filament filament 3
#> gene gene 3
#> glutamate glutamate 3
#> host host 3
#> initiation initiation 3
#> intracellular intracellular 3
#> levels levels 3
#> ligand ligand 3
#> macrophage macrophage 3
#> male male 3
#> maturation maturation 3
#> nerve nerve 3
#> phosphorylation phosphorylation 3
#> potassium potassium 3
#> precursor precursor 3
#> renal renal 3
#> repair repair 3
#> sensory sensory 3
#> signal signal 3
#> spinal spinal 3
#> substrate substrate 3
#> system system 3
#> telomere telomere 3
#> tissue tissue 3
#> transduction transduction 3
#> transition transition 3
#> translation translation 3
#> tubule tubule 3
#> absorption absorption 2
#> acetylation acetylation 2
#> albumin albumin 2
#> alternative alternative 2
#> amyloid amyloid 2
#> antigen antigen 2
#> arterial arterial 2
#> axis axis 2
#> axon axon 2
#> b b 2
#> bile bile 2
#> bundle bundle 2
#> cc cc 2
#> cellcell cellcell 2
#> cells cells 2
#> central central 2
#> centrosome centrosome 2
#> circadian circadian 2
#> commitment commitment 2
#> communication communication 2
#> compact compact 2
#> congression congression 2
#> copper copper 2
#> cortex cortex 2
#> cytoplasmic cytoplasmic 2
#> cytoskeleton cytoskeleton 2
#> death death 2
#> depolarization depolarization 2
#> depolymerization depolymerization 2
#> detection detection 2
#> digestive digestive 2
#> disassembly disassembly 2
#> dnatemplated dnatemplated 2
#> dorsal dorsal 2
#> elongation elongation 2
#> endoderm endoderm 2
#> endoplasmic endoplasmic 2
#> epithelium epithelium 2
#> erad erad 2
#> extrinsic extrinsic 2
#> fate fate 2
#> fiber fiber 2
#> fibroblast fibroblast 2
#> fructose fructose 2
#> gland gland 2
#> glomerular glomerular 2
#> guidance guidance 2
#> healing healing 2
#> highdensity highdensity 2
#> histamine histamine 2
#> hk hk 2
#> hormone hormone 2
#> inflammatory inflammatory 2
#> inositol inositol 2
#> interleukin interleukin 2
#> iron iron 2
#> junction junction 2
#> kinase kinase 2
#> leukocyte leukocyte 2
#> lymphoid lymphoid 2
#> matrix matrix 2
#> mediated mediated 2
#> mesenchymal mesenchymal 2
#> mesoderm mesoderm 2
#> metaphase metaphase 2
#> microglial microglial 2
#> mirna mirna 2
#> modification modification 2
#> modulation modulation 2
#> molecules molecules 2
#> motif motif 2
#> multicellular multicellular 2
#> myocardium myocardium 2
#> necrosis necrosis 2
#> nervous nervous 2
#> nucleus nucleus 2
#> organism organism 2
#> oxidative oxidative 2
#> perception perception 2
#> phosphate phosphate 2
#> phospholipid phospholipid 2
#> plate plate 2
#> polarity polarity 2
#> polymerization polymerization 2
#> postsynaptic postsynaptic 2
#> potential potential 2
#> preinitiation preinitiation 2
#> pressure pressure 2
#> promoter promoter 2
#> proteasomal proteasomal 2
#> pulmonary pulmonary 2
#> reactive reactive 2
#> recognition recognition 2
#> recombination recombination 2
#> remodeling remodeling 2
#> reticulum reticulum 2
#> retrograde retrograde 2
#> segregation segregation 2
#> silencing silencing 2
#> sleep sleep 2
#> sleepwake sleepwake 2
#> somatic somatic 2
#> species species 2
#> specification specification 2
#> sperm sperm 2
#> stress stress 2
#> synaptic synaptic 2
#> synthase synthase 2
#> taste taste 2
#> telomerase telomerase 2
#> telomeric telomeric 2
#> thelper thelper 2
#> tract tract 2
#> transmission transmission 2
#> trisphosphate trisphosphate 2
#> tube tube 2
#> tumor tumor 2
#> type type 2
#> tyrosine tyrosine 2
#> ventricular ventricular 2
#> vesicle vesicle 2
#> wound wound 2
#> acclimation acclimation 1
#> accumbens accumbens 1
#> acetylcholine acetylcholine 1
#> acrosome acrosome 1
#> acrylamide acrylamide 1
#> action action 1
#> activated activated 1
#> acutephase acutephase 1
#> acylglycerol acylglycerol 1
#> adiponectin adiponectin 1
#> adipose adipose 1
#> adrenergic adrenergic 1
#> alkaline alkaline 1
#> alphabeta alphabeta 1
#> aminoacylation aminoacylation 1
#> ammonia ammonia 1
#> ampa ampa 1
#> amyloidbeta amyloidbeta 1
#> anchoring anchoring 1
#> anisomycin anisomycin 1
#> another another 1
#> anterior anterior 1
#> anterograde anterograde 1
#> antigenic antigenic 1
#> antimicrobial antimicrobial 1
#> apicalbasal apicalbasal 1
#> arginase arginase 1
#> arginyltrna arginyltrna 1
#> arm arm 1
#> artery artery 1
#> aspartictype aspartictype 1
#> assimilation assimilation 1
#> asymmetric asymmetric 1
#> atpasecoupled atpasecoupled 1
#> attachment attachment 1
#> auditory auditory 1
#> autophagic autophagic 1
#> autophagy autophagy 1
#> av av 1
#> baseexcision baseexcision 1
#> benzylpenicillin benzylpenicillin 1
#> beta beta 1
#> biotinylation biotinylation 1
#> blue blue 1
#> bombesin bombesin 1
#> branch branch 1
#> break break 1
#> brexanolone brexanolone 1
#> bud bud 1
#> caaxbox caaxbox 1
#> calciumdependent calciumdependent 1
#> cameratype cameratype 1
#> canonical canonical 1
#> cap cap 1
#> capacitation capacitation 1
#> carbon carbon 1
#> cardiolipin cardiolipin 1
#> carnitine carnitine 1
#> cascade cascade 1
#> catabolite catabolite 1
#> catecholamine catecholamine 1
#> cdpositive cdpositive 1
#> cellabiotic cellabiotic 1
#> cellmatrix cellmatrix 1
#> centriole centriole 1
#> centromere centromere 1
#> centromeric centromeric 1
#> ceramide ceramide 1
#> cerebellar cerebellar 1
#> cerebral cerebral 1
#> ceruleus ceruleus 1
#> chamber chamber 1
#> changes changes 1
#> channel channel 1
#> characteristics characteristics 1
#> chemical chemical 1
#> chemokinemediated chemokinemediated 1
#> choline choline 1
#> chondrocyte chondrocyte 1
#> chromatid chromatid 1
#> chromatin chromatin 1
#> cilium cilium 1
#> circulatory circulatory 1
#> citrate citrate 1
#> class class 1
#> clathrindependent clathrindependent 1
#> clearance clearance 1
#> cleavage cleavage 1
#> cluster cluster 1
#> coagulation coagulation 1
#> coenzyme coenzyme 1
#> cohesion cohesion 1
#> collecting collecting 1
#> colonystimulating colonystimulating 1
#> complement complement 1
#> compound compound 1
#> conduction conduction 1
#> connecting connecting 1
#> constitutive constitutive 1
#> contraction contraction 1
#> core core 1
#> cornification cornification 1
#> cortisol cortisol 1
#> costimulation costimulation 1
#> cotranslational cotranslational 1
#> coupled coupled 1
#> coupling coupling 1
#> crosslink crosslink 1
#> cterminal cterminal 1
#> cyclase cyclase 1
#> cyclaseactivating cyclaseactivating 1
#> cyclaseinhibiting cyclaseinhibiting 1
#> cytokinemediated cytokinemediated 1
#> cytokinesis cytokinesis 1
#> cytosol cytosol 1
#> cytotoxicity cytotoxicity 1
#> deacetylation deacetylation 1
#> decreased decreased 1
#> demethylation demethylation 1
#> dendritic dendritic 1
#> dentincontaining dentincontaining 1
#> deoxyribonucleoside deoxyribonucleoside 1
#> dephosphorylation dephosphorylation 1
#> detoxification detoxification 1
#> developmental developmental 1
#> dgtp dgtp 1
#> dibasic dibasic 1
#> dipeptide dipeptide 1
#> dispersal dispersal 1
#> distal distal 1
#> diterpenoid diterpenoid 1
#> diversification diversification 1
#> dloop dloop 1
#> doublestrand doublestrand 1
#> doxorubicin doxorubicin 1
#> dsrna dsrna 1
#> duct duct 1
#> dump dump 1
#> dynein dynein 1
#> early early 1
#> ectodermal ectodermal 1
#> edge edge 1
#> electrical electrical 1
#> electron electron 1
#> end end 1
#> endocardium endocardium 1
#> endochondral endochondral 1
#> endocytosis endocytosis 1
#> endopeptidase endopeptidase 1
#> engulfment engulfment 1
#> envelope envelope 1
#> eosinophil eosinophil 1
#> epinephrine epinephrine 1
#> er er 1
#> ergic ergic 1
#> erythrocyte erythrocyte 1
#> esterification esterification 1
#> estrogen estrogen 1
#> ethanol ethanol 1
#> eukaryotic eukaryotic 1
#> excretion excretion 1
#> exogenous exogenous 1
#> expression expression 1
#> eye eye 1
#> fad fad 1
#> fasciculation fasciculation 1
#> fat fat 1
#> fc fc 1
#> female female 1
#> fes fes 1
#> fibril fibril 1
#> fibronectin fibronectin 1
#> fluid fluid 1
#> follicle follicle 1
#> forelimb forelimb 1
#> form form 1
#> g g 1
#> generation generation 1
#> genitalia genitalia 1
#> genome genome 1
#> glucocorticoid glucocorticoid 1
#> gluconeogenesis gluconeogenesis 1
#> glucose glucose 1
#> glucosylceramide glucosylceramide 1
#> glycine glycine 1
#> glyoxylate glyoxylate 1
#> gmi gmi 1
#> gonad gonad 1
#> gonadotropin gonadotropin 1
#> granule granule 1
#> granuloma granuloma 1
#> granzymemediated granzymemediated 1
#> guanine guanine 1
#> ha ha 1
#> hair hair 1
#> heart heart 1
#> heat heat 1
#> hematopoietic hematopoietic 1
#> hepatic hepatic 1
#> hepatocyte hepatocyte 1
#> heterochromatin heterochromatin 1
#> hh hh 1
#> hippo hippo 1
#> homeostatic homeostatic 1
#> homologous homologous 1
#> homophilic homophilic 1
#> hr hr 1
#> hs hs 1
#> hydroxyurea hydroxyurea 1
#> hypertrophy hypertrophy 1
#> hypotonic hypotonic 1
#> ii ii 1
#> iii iii 1
#> immunoglobulin immunoglobulin 1
#> impulse impulse 1
#> induced induced 1
#> induction induction 1
#> inhibition inhibition 1
#> inhibitory inhibitory 1
#> inner inner 1
#> insulin insulin 1
#> integrin integrin 1
#> integrity integrity 1
#> interferonalpha interferonalpha 1
#> interkinetic interkinetic 1
#> intermediate intermediate 1
#> intermediatedensity intermediatedensity 1
#> intermembrane intermembrane 1
#> interneuron interneuron 1
#> interstrand interstrand 1
#> intrinsic intrinsic 1
#> intron intron 1
#> involuntary involuntary 1
#> iodide iodide 1
#> ionizing ionizing 1
#> isotype isotype 1
#> joining joining 1
#> kallikreinkinin kallikreinkinin 1
#> kappab kappab 1
#> keratinocyte keratinocyte 1
#> ketone ketone 1
#> killing killing 1
#> kinasenfkappab kinasenfkappab 1
#> lactate lactate 1
#> lateral lateral 1
#> lead lead 1
#> leading leading 1
#> lhistidine lhistidine 1
#> light light 1
#> lineage lineage 1
#> lipopolysaccharide lipopolysaccharide 1
#> lithium lithium 1
#> locus locus 1
#> loop loop 1
#> lowdensity lowdensity 1
#> lung lung 1
#> lymphocyte lymphocyte 1
#> lymphotoxin lymphotoxin 1
#> lysosome lysosome 1
#> magnesium magnesium 1
#> malonate malonate 1
#> mammary mammary 1
#> mass mass 1
#> mast mast 1
#> maternal maternal 1
#> mediator mediator 1
#> mediumchain mediumchain 1
#> meiosis meiosis 1
#> member member 1
#> mesangial mesangial 1
#> mesenchymalepithelial mesenchymalepithelial 1
#> mesenchyme mesenchyme 1
#> methylglyoxal methylglyoxal 1
#> minusenddirected minusenddirected 1
#> mirnamediated mirnamediated 1
#> mirnas mirnas 1
#> monophosphate monophosphate 1
#> motor motor 1
#> multivesicular multivesicular 1
#> muramyl muramyl 1
#> mutation mutation 1
#> myeloid myeloid 1
#> myocyte myocyte 1
#> myotube myotube 1
#> nacetylglucosamine nacetylglucosamine 1
#> nail nail 1
#> ncrna ncrna 1
#> nephron nephron 1
#> netrinactivated netrinactivated 1
#> network network 1
#> neurofilament neurofilament 1
#> neuromast neuromast 1
#> neuropeptide neuropeptide 1
#> neurotransmitter neurotransmitter 1
#> neutrophil neutrophil 1
#> nfkappabinducing nfkappabinducing 1
#> nglycosylase nglycosylase 1
#> niknfkappab niknfkappab 1
#> nitric nitric 1
#> nodal nodal 1
#> node node 1
#> nonhomologous nonhomologous 1
#> nonrem nonrem 1
#> notch notch 1
#> nterminal nterminal 1
#> nucleobase nucleobase 1
#> nucleoside nucleoside 1
#> oacetyltransferase oacetyltransferase 1
#> odontogenesis odontogenesis 1
#> oogenesis oogenesis 1
#> open open 1
#> optic optic 1
#> orbitofrontal orbitofrontal 1
#> organismal organismal 1
#> organs organs 1
#> ossification ossification 1
#> osteoblast osteoblast 1
#> outer outer 1
#> ovarian ovarian 1
#> ovulation ovulation 1
#> oxaloacetate oxaloacetate 1
#> oxide oxide 1
#> p p 1
#> pain pain 1
#> palate palate 1
#> pancreatic pancreatic 1
#> paranodal paranodal 1
#> parietal parietal 1
#> pattern pattern 1
#> peptidase peptidase 1
#> peptide peptide 1
#> peptidylaspartic peptidylaspartic 1
#> peptidylhistidine peptidylhistidine 1
#> peroxisome peroxisome 1
#> ph ph 1
#> phagocytosis phagocytosis 1
#> phase phase 1
#> phosphatase phosphatase 1
#> phosphatecontaining phosphatecontaining 1
#> phosphatidylethanolamine phosphatidylethanolamine 1
#> phosphoadenosine phosphoadenosine 1
#> phosphosulfate phosphosulfate 1
#> photoreceptor photoreceptor 1
#> pigmentation pigmentation 1
#> placenta placenta 1
#> planar planar 1
#> polyadenylation polyadenylation 1
#> polyadpribosylation polyadpribosylation 1
#> population population 1
#> postembryonic postembryonic 1
#> preantral preantral 1
#> premirna premirna 1
#> preribosome preribosome 1
#> presentation presentation 1
#> primary primary 1
#> primitive primitive 1
#> projection projection 1
#> prolactin prolactin 1
#> pronucleus pronucleus 1
#> proofreading proofreading 1
#> proteasome proteasome 1
#> proteincoupled proteincoupled 1
#> proteindna proteindna 1
#> proton proton 1
#> protontransporting protontransporting 1
#> proximal proximal 1
#> proximaldistal proximaldistal 1
#> pseudouridine pseudouridine 1
#> purkinje purkinje 1
#> radiation radiation 1
#> receptors receptors 1
#> recycling recycling 1
#> regionalization regionalization 1
#> regulatory regulatory 1
#> release release 1
#> replicationindependent replicationindependent 1
#> replicative replicative 1
#> repolarization repolarization 1
#> respiration respiration 1
#> retina retina 1
#> retrotrapezoid retrotrapezoid 1
#> reverse reverse 1
#> rho rho 1
#> rhythm rhythm 1
#> ribbon ribbon 1
#> ribonucleoprotein ribonucleoprotein 1
#> ribosomal ribosomal 1
#> right right 1
#> rnabinding rnabinding 1
#> rnatemplated rnatemplated 1
#> s s 1
#> salivary salivary 1
#> secondary secondary 1
#> secreting secreting 1
#> secretory secretory 1
#> self self 1
#> semaphorinplexin semaphorinplexin 1
#> senescence senescence 1
#> septin septin 1
#> septum septum 1
#> sequestering sequestering 1
#> serinetype serinetype 1
#> sexual sexual 1
#> shortchain shortchain 1
#> sister sister 1
#> site site 1
#> skeletal skeletal 1
#> somatostatin somatostatin 1
#> sorting sorting 1
#> space space 1
#> spermidine spermidine 1
#> splice splice 1
#> spliceosome spliceosome 1
#> splicing splicing 1
#> spreading spreading 1
#> srpdependent srpdependent 1
#> stability stability 1
#> stellate stellate 1
#> stem stem 1
#> stimulatory stimulatory 1
#> storeoperated storeoperated 1
#> stressinduced stressinduced 1
#> substratedependent substratedependent 1
#> succinate succinate 1
#> sumo sumo 1
#> sumoylation sumoylation 1
#> superfamily superfamily 1
#> supramolecular supramolecular 1
#> surface surface 1
#> switching switching 1
#> symmetric symmetric 1
#> sympathetic sympathetic 1
#> synthesis synthesis 1
#> systemic systemic 1
#> target target 1
#> targeting targeting 1
#> telemethylhistidine telemethylhistidine 1
#> termination termination 1
#> testosterone testosterone 1
#> thermogenesis thermogenesis 1
#> thrombinactivated thrombinactivated 1
#> thymus thymus 1
#> thyroid thyroid 1
#> tolerance tolerance 1
#> tolllike tolllike 1
#> tooth tooth 1
#> torc torc 1
#> touch touch 1
#> trachea trachea 1
#> transcriptase transcriptase 1
#> transfer transfer 1
#> transferase transferase 1
#> transforming transforming 1
#> transsynaptic transsynaptic 1
#> triglyceride triglyceride 1
#> trimethylhkspecific trimethylhkspecific 1
#> triphosphate triphosphate 1
#> trna trna 1
#> trnatype trnatype 1
#> trophectodermal trophectodermal 1
#> trophoblast trophoblast 1
#> tubular tubular 1
#> tubulin tubulin 1
#> ubiquitination ubiquitination 1
#> ubiquitindependent ubiquitindependent 1
#> udpnacetylgalactosamine udpnacetylgalactosamine 1
#> ultradian ultradian 1
#> unfolded unfolded 1
#> unwinding unwinding 1
#> uracil uracil 1
#> urate urate 1
#> urea urea 1
#> uvb uvb 1
#> valine valine 1
#> vascular vascular 1
#> vdj vdj 1
#> ventricle ventricle 1
#> vessel vessel 1
#> virion virion 1
#> wnt wnt 1
#> wounding wounding 1
#> xenophagy xenophagy 1
#> xii xii 1