The function ctr_df generates a data.frame containing the degree of nodes for each layer.
ctr_df.RdThe function ctr_df generates a data.frame containing the degree of nodes for each layer.
Value
Returns a data.frame with centrality value (if preprocessed with ctr_ml or ctr_g: degree, betweenness or closeness), p_tax and g_tax of each node (the function takes this info from ml_TaxGroup).
Examples
#Load the example net
data ("mlTaxGroup_dstool")
# Create a vector with layers' names
v <- c("sample A", "sample B")
ctr_df (mlTaxGroup_dstool, layer_names = v)
#> sample A sample B p_tax
#> 1 1 0 Nitrospiraceae
#> 2 0 0 none
#> 3 0 0 Rikenellaceae
#> 4 0 0 Porphyromonadaceae
#> 5 0 0 Bacteroidaceae
#> 6 0 0 Prevotellaceae
#> 7 0 0 Flavobacteriaceae
#> 8 0 4 Acidobacteriaceae
#> 9 0 0 Spirochaetaceae
#> 10 0 0 Hyphomicrobiaceae
#> 11 0 0 Bradyrhizobiaceae
#> 12 0 0 Xanthobacteraceae
#> 13 0 0 Methylobacteriaceae
#> 14 0 0 Rhizobiaceae
#> 15 0 0 Caulobacteraceae
#> 16 0 0 Rhodobacteraceae
#> 17 0 0 Sphingomonadaceae
#> 18 0 0 Neisseriaceae
#> 19 0 0 Rhodocyclaceae
#> 20 0 0 Alcaligenaceae
#> 21 0 0 Comamonadaceae
#> 22 0 0 Burkholderiaceae
#> 23 0 0 Oxalobacteraceae
#> 24 0 0 Cardiobacteriaceae
#> 25 0 3 Oceanospirillaceae
#> 26 0 0 Moraxellaceae
#> 27 0 0 Pseudomonadaceae
#> 28 0 0 Pseudoalteromonadaceae
#> 29 0 0 Shewanellaceae
#> 30 0 0 Vibrionaceae
#> 31 0 0 Pasteurellaceae
#> 32 0 0 Enterobacteriaceae
#> 33 0 0 Desulfovibrionaceae
#> 34 0 0 Campylobacteraceae
#> 35 0 0 Fusobacteriaceae
#> 36 0 0 Coriobacteriaceae
#> 37 0 0 Geodermatophilaceae
#> 38 0 0 Frankiaceae
#> 39 0 0 Microbacteriaceae
#> 40 0 0 Cellulomonadaceae
#> 41 0 0 Intrasporangiaceae
#> 42 0 0 Micrococcaceae
#> 43 0 0 Dermabacteraceae
#> 44 0 0 Dermacoccaceae
#> 45 0 0 Actinomycetaceae
#> 46 0 0 Bifidobacteriaceae
#> 47 0 0 Propionibacteriaceae
#> 48 0 0 Mycobacteriaceae
#> 49 0 0 Gordoniaceae
#> 50 0 0 Corynebacteriaceae
#> 51 0 0 Nocardiaceae
#> 52 0 0 Veillonellaceae
#> 53 0 0 Peptococcaceae
#> 54 0 0 Lachnospiraceae
#> 55 0 0 ClostridialesFamilyXIII.IncertaeSedis
#> 56 0 0 Clostridiaceae
#> 57 0 0 Peptostreptococcaceae
#> 58 0 0 ClostridialesFamilyXI.IncertaeSedis
#> 59 0 0 Paenibacillaceae
#> 60 0 0 Bacillaceae
#> 61 0 0 Planococcaceae
#> 62 0 0 Gemellaceae
#> 63 0 0 Aerococcaceae
#> 64 0 0 Carnobacteriaceae
#> 65 0 0 Leuconostocaceae
#> 66 0 0 Lactobacillaceae
#> 67 0 0 Enterococcaceae
#> 68 0 0 Streptococcaceae
#> 69 0 0 Erysipelotrichaceae
#> 70 0 0 Ruminococcaceae
#> 71 0 0 Staphylococcaceae
#> 72 0 0 Coxiellaceae
#> 73 0 0 Nocardioidaceae
#> 74 0 0 Brucellaceae
#> 75 0 0 Flexibacteraceae
#> 76 0 0 Turicibacteraceae
#> 77 1 0 Tsukamurellaceae
#> 78 0 0 Phyllobacteriaceae
#> 79 0 0 Brevibacteriaceae
#> 80 0 0 Aeromonadaceae
#> 81 0 4 Sinobacteraceae
#> 82 0 0 Beijerinckiaceae
#> 83 0 0 Catabacteriaceae
#> 84 0 0 Dietziaceae
#> 85 0 0 Pseudonocardiaceae
#> 86 0 0 F16
#> 87 0 0 Halomonadaceae
#> 88 0 0 Xanthomonadaceae
#> 89 0 0 Sphingobacteriaceae
#> 90 0 0 Alteromonadaceae
#> 91 0 0 Dethiosulfovibrionaceae
#> 92 0 0 Thermaceae
#> 93 0 3 Bacteriovoracaceae
#> 94 0 0 Acetobacteraceae
#> 95 0 0 Nostocaceae
#> 96 0 0 Colwelliaceae
#> 97 0 1 Planctomycetaceae
#> 98 0 0 Hydrogenophilaceae
#> 99 0 0 Nocardiopsaceae
#> 100 0 0 Rhodospirillaceae
#> 101 0 3 Methylophilaceae
#> 102 0 0 Promicromonosporaceae
#> 103 0 0 OM60
#> 104 0 0 Cryomorphaceae
#> 105 0 3 Methylocystaceae
#> 106 0 0 Bdellovibrionaceae
#> 107 0 4 Streptomycetaceae
#> 108 1 0 Hyphomonadaceae
#> 109 0 0 Solibacteraceae
#> 110 0 0 Rubrobacteraceae
#> 111 0 0 Chromatiaceae
#> 112 0 0 Bogoriellaceae
#> 113 0 0 Williamsiaceae
#> 114 0 0 Legionellaceae
#> 115 1 0 Gallionellaceae
#> 116 1 0 Armatimonadaceae
#> 117 0 0 Opitutaceae
#> 118 1 0 Alicyclobacillaceae
#> 119 0 0 Solirubrobacteraceae
#> 120 0 4 Spartobacteriaceae
#> 121 0 0 Aurantimonadaceae
#> 122 0 0 Gemmatimonadaceae
#> 123 0 4 Micromonosporaceae
#> 124 0 0 Saccharospirillaceae
#> 125 0 0 Xenococcaceae
#> 126 0 0 Verrucomicrobiaceae
#> 127 0 0 Dermatophilaceae
#> 128 0 0 Listeriaceae
#> 129 0 0 Psychromonadaceae
#> 130 0 0 Gemmataceae
#> 131 0 0 Syntrophobacteraceae
#> 132 0 0 Haliangiaceae
#> 133 0 0 Idiomarinaceae
#> 134 0 0 Dehalobacteriaceae
#> 135 0 1 AKIW874
#> 136 1 0 ACK-M1
#> 137 0 0 Eubacteriaceae
#> 138 0 0 Deinococcaceae
#> 139 0 0 Leptospiraceae
#> 140 1 0 ThermoanaerobacteralesFamilyIII.IncertaeSedis
#> 141 0 0 Nitrosomonadaceae
#> 142 0 0 Erythrobacteraceae
#> 143 0 0 Thermicanaceae
#> 144 0 0 Victivallaceae
#> 145 0 0 A29
#> 146 0 0 Rhodothermaceae
#> 147 0 0 Helicobacteraceae
#> 148 0 0 Exiguobacteraceae
#> 149 0 0 Patulibacteraceae
#> 150 0 0 Methanobacteriaceae
#> 151 0 0 Sanguibacteraceae
#> 152 0 0 Phormidiaceae
#> g_tax
#> 1 Nitrospirae
#> 2 BRC1
#> 3 Bacteroidetes
#> 4 Bacteroidetes
#> 5 Bacteroidetes
#> 6 Bacteroidetes
#> 7 Bacteroidetes
#> 8 Acidobacteria (phylum)
#> 9 Spirochaetes (phylum)
#> 10 Proteobacteria
#> 11 Proteobacteria
#> 12 Proteobacteria
#> 13 Proteobacteria
#> 14 Proteobacteria
#> 15 Proteobacteria
#> 16 Proteobacteria
#> 17 Proteobacteria
#> 18 Proteobacteria
#> 19 Proteobacteria
#> 20 Proteobacteria
#> 21 Proteobacteria
#> 22 Proteobacteria
#> 23 Proteobacteria
#> 24 Proteobacteria
#> 25 Proteobacteria
#> 26 Proteobacteria
#> 27 Proteobacteria
#> 28 Proteobacteria
#> 29 Proteobacteria
#> 30 Proteobacteria
#> 31 Proteobacteria
#> 32 Proteobacteria
#> 33 Proteobacteria
#> 34 Proteobacteria
#> 35 Fusobacteria (phylum)
#> 36 Actinobacteria (phylum)
#> 37 Actinobacteria (phylum)
#> 38 Actinobacteria (phylum)
#> 39 Actinobacteria (phylum)
#> 40 Actinobacteria (phylum)
#> 41 Actinobacteria (phylum)
#> 42 Actinobacteria (phylum)
#> 43 Actinobacteria (phylum)
#> 44 Actinobacteria (phylum)
#> 45 Actinobacteria (phylum)
#> 46 Actinobacteria (phylum)
#> 47 Actinobacteria (phylum)
#> 48 Actinobacteria (phylum)
#> 49 Actinobacteria (phylum)
#> 50 Actinobacteria (phylum)
#> 51 Actinobacteria (phylum)
#> 52 Firmicutes
#> 53 Firmicutes
#> 54 Firmicutes
#> 55 Firmicutes
#> 56 Firmicutes
#> 57 Firmicutes
#> 58 Firmicutes
#> 59 Firmicutes
#> 60 Firmicutes
#> 61 Firmicutes
#> 62 Firmicutes
#> 63 Firmicutes
#> 64 Firmicutes
#> 65 Firmicutes
#> 66 Firmicutes
#> 67 Firmicutes
#> 68 Firmicutes
#> 69 Tenericutes
#> 70 Firmicutes
#> 71 Firmicutes
#> 72 Proteobacteria
#> 73 Actinobacteria (phylum)
#> 74 Proteobacteria
#> 75 Bacteroidetes
#> 76 Firmicutes
#> 77 Actinobacteria (phylum)
#> 78 Proteobacteria
#> 79 Actinobacteria (phylum)
#> 80 Proteobacteria
#> 81 Proteobacteria
#> 82 Proteobacteria
#> 83 Firmicutes
#> 84 Actinobacteria (phylum)
#> 85 Actinobacteria (phylum)
#> 86 TM7
#> 87 Proteobacteria
#> 88 Proteobacteria
#> 89 Bacteroidetes
#> 90 Proteobacteria
#> 91 Synergistetes
#> 92 Thermi
#> 93 Proteobacteria
#> 94 Proteobacteria
#> 95 Cyanobacteria
#> 96 Proteobacteria
#> 97 Planctomycetes
#> 98 Proteobacteria
#> 99 Actinobacteria (phylum)
#> 100 Proteobacteria
#> 101 Proteobacteria
#> 102 Actinobacteria (phylum)
#> 103 Proteobacteria
#> 104 Bacteroidetes
#> 105 Proteobacteria
#> 106 Proteobacteria
#> 107 Actinobacteria (phylum)
#> 108 Proteobacteria
#> 109 Acidobacteria (phylum)
#> 110 Actinobacteria (phylum)
#> 111 Proteobacteria
#> 112 Actinobacteria (phylum)
#> 113 Actinobacteria (phylum)
#> 114 Proteobacteria
#> 115 Proteobacteria
#> 116 Armatimonadetes
#> 117 Verrucomicrobia
#> 118 Firmicutes
#> 119 Actinobacteria (phylum)
#> 120 Verrucomicrobia
#> 121 Proteobacteria
#> 122 Gemmatimonadetes (phylum)
#> 123 Actinobacteria (phylum)
#> 124 Proteobacteria
#> 125 Cyanobacteria
#> 126 Verrucomicrobia
#> 127 Actinobacteria (phylum)
#> 128 Firmicutes
#> 129 Proteobacteria
#> 130 Planctomycetes
#> 131 Proteobacteria
#> 132 Proteobacteria
#> 133 Proteobacteria
#> 134 Firmicutes
#> 135 Actinobacteria (phylum)
#> 136 Actinobacteria (phylum)
#> 137 Firmicutes
#> 138 Thermi
#> 139 Spirochaetes (phylum)
#> 140 Firmicutes
#> 141 Proteobacteria
#> 142 Proteobacteria
#> 143 Firmicutes
#> 144 Lentisphaerae
#> 145 TM7
#> 146 Bacteroidetes
#> 147 Proteobacteria
#> 148 Firmicutes
#> 149 Actinobacteria (phylum)
#> 150 Euryarchaeota
#> 151 Actinobacteria (phylum)
#> 152 Cyanobacteria