Create a long data.frame with grouped abundances from a MultiAssayExperiment counts object
Source:R/get_stacked_data.R
get_stacked_data.RdThis function takes a MultiAssayExperiment object and a specified
taxon level of interest and creates a long data.frame that can be used
more easily for plotting counts data in a stacked bar plot or a stacked area
chart. The function groups taxa and computes relative abundance within taxa strata.
Arguments
- dat
A
MultiAssayExperimentobject specially formatted as an animalcules output.- taxon_level
Character string indicating the level of taxonomy to aggregate the counts data. Must be the name of a column in
MultiAssayExperiment::rowData(dat).- covariate_1
Character string, the name of the covariate in `dat` by which to color and group samples. Default is
NULL.- covariate_time
Character string giving the name of the discrete time-based covariate in the metadata to group abundances by.
Examples
in_dat <- system.file("extdata/MAE_small.RDS", package = "LegATo") |> readRDS()
get_stacked_data(in_dat, "genus", covariate_1 = "Sex", covariate_time = "Month")
#> taxon covariate_1 covariate_t value
#> 1 Acinetobacter Female 1 5.391689e-01
#> 2 Aeromonas Female 1 2.438339e-03
#> 3 Alkalihalophilus Female 1 9.691706e-03
#> 4 Brucella Female 1 7.903853e-03
#> 5 Corynebacterium Female 1 5.658341e-02
#> 6 Cutibacterium Female 1 3.254340e-06
#> 7 Delftia Female 1 5.878204e-04
#> 8 Dolosigranulum Female 1 2.097972e-03
#> 9 Enterobacter Female 1 5.019068e-02
#> 10 Escherichia Female 1 0.000000e+00
#> 11 Haemophilus Female 1 6.461345e-03
#> 12 Kocuria Female 1 1.636577e-02
#> 13 Listeria Female 1 5.812874e-02
#> 14 Moraxella Female 1 1.659765e-02
#> 15 Mycoplasma Female 1 1.337991e-03
#> 16 Noviherbaspirillum Female 1 3.339523e-02
#> 17 Other Female 1 7.158095e-03
#> 18 Paracoccus Female 1 2.638631e-04
#> 19 Pseudomonas Female 1 5.979654e-02
#> 20 Staphylococcus Female 1 1.060623e-01
#> 21 Streptococcus Female 1 1.022373e-02
#> 22 Weissella Female 1 1.554279e-02
#> 23 Acinetobacter Male 1 7.186046e-01
#> 24 Aeromonas Male 1 2.558981e-03
#> 25 Alkalihalophilus Male 1 5.785040e-03
#> 26 Brucella Male 1 1.301520e-02
#> 27 Corynebacterium Male 1 5.996756e-02
#> 28 Cutibacterium Male 1 0.000000e+00
#> 29 Delftia Male 1 2.019060e-04
#> 30 Dolosigranulum Male 1 0.000000e+00
#> 31 Enterobacter Male 1 8.146629e-04
#> 32 Escherichia Male 1 1.717688e-04
#> 33 Haemophilus Male 1 1.861050e-03
#> 34 Kocuria Male 1 1.676032e-02
#> 35 Listeria Male 1 4.135671e-02
#> 36 Moraxella Male 1 1.825386e-02
#> 37 Mycoplasma Male 1 0.000000e+00
#> 38 Noviherbaspirillum Male 1 1.885875e-02
#> 39 Other Male 1 3.330495e-03
#> 40 Paracoccus Male 1 1.210947e-04
#> 41 Pseudomonas Male 1 2.097881e-02
#> 42 Staphylococcus Male 1 2.859913e-02
#> 43 Streptococcus Male 1 7.354020e-03
#> 44 Weissella Male 1 4.140605e-02
#> 45 Acinetobacter Female 2 2.891848e-01
#> 46 Aeromonas Female 2 3.293784e-03
#> 47 Alkalihalophilus Female 2 2.061783e-02
#> 48 Brucella Female 2 1.184035e-01
#> 49 Corynebacterium Female 2 2.085925e-01
#> 50 Cutibacterium Female 2 2.319900e-04
#> 51 Delftia Female 2 0.000000e+00
#> 52 Dolosigranulum Female 2 2.334195e-04
#> 53 Enterobacter Female 2 4.474153e-03
#> 54 Escherichia Female 2 3.616898e-05
#> 55 Haemophilus Female 2 7.602519e-03
#> 56 Kocuria Female 2 5.997889e-02
#> 57 Listeria Female 2 1.571650e-02
#> 58 Moraxella Female 2 2.717076e-03
#> 59 Mycoplasma Female 2 2.120441e-04
#> 60 Noviherbaspirillum Female 2 5.206077e-02
#> 61 Other Female 2 1.715177e-03
#> 62 Paracoccus Female 2 1.221874e-03
#> 63 Pseudomonas Female 2 2.581273e-02
#> 64 Staphylococcus Female 2 1.551813e-01
#> 65 Streptococcus Female 2 2.197573e-02
#> 66 Weissella Female 2 1.073722e-02
#> 67 Acinetobacter Male 2 1.999837e-01
#> 68 Aeromonas Male 2 6.493406e-03
#> 69 Alkalihalophilus Male 2 4.080035e-02
#> 70 Brucella Male 2 0.000000e+00
#> 71 Corynebacterium Male 2 2.927187e-01
#> 72 Cutibacterium Male 2 0.000000e+00
#> 73 Delftia Male 2 5.355868e-04
#> 74 Dolosigranulum Male 2 4.088307e-04
#> 75 Enterobacter Male 2 1.424023e-02
#> 76 Escherichia Male 2 0.000000e+00
#> 77 Haemophilus Male 2 0.000000e+00
#> 78 Kocuria Male 2 7.883521e-02
#> 79 Listeria Male 2 8.806327e-03
#> 80 Moraxella Male 2 9.599653e-03
#> 81 Mycoplasma Male 2 1.482604e-03
#> 82 Noviherbaspirillum Male 2 1.252488e-01
#> 83 Other Male 2 3.985658e-02
#> 84 Paracoccus Male 2 3.379633e-03
#> 85 Pseudomonas Male 2 3.334081e-02
#> 86 Staphylococcus Male 2 1.155584e-01
#> 87 Streptococcus Male 2 2.810115e-02
#> 88 Weissella Male 2 6.099738e-04
#> 89 Acinetobacter Female 3 6.499687e-01
#> 90 Aeromonas Female 3 2.236433e-03
#> 91 Alkalihalophilus Female 3 1.882353e-02
#> 92 Brucella Female 3 2.520446e-02
#> 93 Corynebacterium Female 3 5.835613e-02
#> 94 Cutibacterium Female 3 1.988599e-04
#> 95 Delftia Female 3 0.000000e+00
#> 96 Dolosigranulum Female 3 4.770992e-04
#> 97 Enterobacter Female 3 3.162774e-04
#> 98 Escherichia Female 3 0.000000e+00
#> 99 Haemophilus Female 3 2.275651e-03
#> 100 Kocuria Female 3 5.001987e-02
#> 101 Listeria Female 3 1.093955e-02
#> 102 Moraxella Female 3 9.422491e-03
#> 103 Mycoplasma Female 3 0.000000e+00
#> 104 Noviherbaspirillum Female 3 5.850758e-02
#> 105 Other Female 3 8.480622e-03
#> 106 Paracoccus Female 3 7.002915e-04
#> 107 Pseudomonas Female 3 1.428963e-02
#> 108 Staphylococcus Female 3 4.560926e-02
#> 109 Streptococcus Female 3 2.034611e-02
#> 110 Weissella Female 3 2.382747e-02
#> 111 Acinetobacter Male 3 3.981444e-01
#> 112 Aeromonas Male 3 4.853417e-03
#> 113 Alkalihalophilus Male 3 1.966537e-02
#> 114 Brucella Male 3 2.308467e-04
#> 115 Corynebacterium Male 3 3.140045e-01
#> 116 Cutibacterium Male 3 0.000000e+00
#> 117 Delftia Male 3 2.364092e-05
#> 118 Dolosigranulum Male 3 0.000000e+00
#> 119 Enterobacter Male 3 1.154233e-04
#> 120 Escherichia Male 3 0.000000e+00
#> 121 Haemophilus Male 3 4.694783e-03
#> 122 Kocuria Male 3 5.619978e-02
#> 123 Listeria Male 3 5.486090e-03
#> 124 Moraxella Male 3 9.738111e-03
#> 125 Mycoplasma Male 3 0.000000e+00
#> 126 Noviherbaspirillum Male 3 7.001699e-02
#> 127 Other Male 3 2.225028e-05
#> 128 Paracoccus Male 3 9.047289e-04
#> 129 Pseudomonas Male 3 2.237977e-02
#> 130 Staphylococcus Male 3 7.795437e-02
#> 131 Streptococcus Male 3 9.372974e-03
#> 132 Weissella Male 3 6.192548e-03
#> 133 Acinetobacter Female 4 2.452786e-01
#> 134 Aeromonas Female 4 3.086301e-03
#> 135 Alkalihalophilus Female 4 3.376783e-02
#> 136 Brucella Female 4 8.995811e-05
#> 137 Corynebacterium Female 4 4.324418e-01
#> 138 Cutibacterium Female 4 0.000000e+00
#> 139 Delftia Female 4 1.028093e-05
#> 140 Dolosigranulum Female 4 2.008520e-04
#> 141 Enterobacter Female 4 4.476406e-05
#> 142 Escherichia Female 4 9.820426e-06
#> 143 Haemophilus Female 4 5.577735e-03
#> 144 Kocuria Female 4 8.218467e-02
#> 145 Listeria Female 4 6.245263e-03
#> 146 Moraxella Female 4 1.310476e-03
#> 147 Mycoplasma Female 4 1.916964e-05
#> 148 Noviherbaspirillum Female 4 1.018919e-01
#> 149 Other Female 4 3.873295e-04
#> 150 Paracoccus Female 4 7.560971e-04
#> 151 Pseudomonas Female 4 2.241424e-02
#> 152 Staphylococcus Female 4 5.451741e-02
#> 153 Streptococcus Female 4 1.804766e-03
#> 154 Weissella Female 4 7.960703e-03
#> 155 Acinetobacter Male 4 3.639182e-01
#> 156 Aeromonas Male 4 3.759683e-03
#> 157 Alkalihalophilus Male 4 2.856256e-02
#> 158 Brucella Male 4 1.373995e-02
#> 159 Corynebacterium Male 4 2.573700e-01
#> 160 Cutibacterium Male 4 0.000000e+00
#> 161 Delftia Male 4 0.000000e+00
#> 162 Dolosigranulum Male 4 1.173147e-03
#> 163 Enterobacter Male 4 1.602598e-03
#> 164 Escherichia Male 4 8.383635e-05
#> 165 Haemophilus Male 4 1.417828e-03
#> 166 Kocuria Male 4 9.316342e-02
#> 167 Listeria Male 4 1.135734e-03
#> 168 Moraxella Male 4 7.655696e-03
#> 169 Mycoplasma Male 4 0.000000e+00
#> 170 Noviherbaspirillum Male 4 7.109326e-02
#> 171 Other Male 4 5.361930e-03
#> 172 Paracoccus Male 4 7.002801e-04
#> 173 Pseudomonas Male 4 1.543425e-02
#> 174 Staphylococcus Male 4 9.262638e-02
#> 175 Streptococcus Male 4 5.947442e-03
#> 176 Weissella Male 4 3.525386e-02
#> 177 Acinetobacter Female 5 4.984428e-01
#> 178 Aeromonas Female 5 4.407478e-03
#> 179 Alkalihalophilus Female 5 2.382268e-02
#> 180 Brucella Female 5 1.965445e-02
#> 181 Corynebacterium Female 5 7.248403e-02
#> 182 Cutibacterium Female 5 1.622850e-04
#> 183 Delftia Female 5 7.631683e-04
#> 184 Dolosigranulum Female 5 2.855837e-04
#> 185 Enterobacter Female 5 2.046007e-03
#> 186 Escherichia Female 5 0.000000e+00
#> 187 Haemophilus Female 5 1.095410e-02
#> 188 Kocuria Female 5 8.403286e-02
#> 189 Listeria Female 5 1.334244e-03
#> 190 Moraxella Female 5 5.641280e-02
#> 191 Mycoplasma Female 5 4.057124e-04
#> 192 Noviherbaspirillum Female 5 7.468856e-02
#> 193 Other Female 5 1.380452e-02
#> 194 Paracoccus Female 5 7.857236e-03
#> 195 Pseudomonas Female 5 2.493605e-02
#> 196 Staphylococcus Female 5 8.655116e-02
#> 197 Streptococcus Female 5 5.756125e-03
#> 198 Weissella Female 5 1.119812e-02
#> 199 Acinetobacter Male 5 4.782496e-01
#> 200 Aeromonas Male 5 3.048189e-03
#> 201 Alkalihalophilus Male 5 1.903549e-02
#> 202 Brucella Male 5 3.601268e-04
#> 203 Corynebacterium Male 5 6.770415e-02
#> 204 Cutibacterium Male 5 0.000000e+00
#> 205 Delftia Male 5 9.363296e-04
#> 206 Dolosigranulum Male 5 0.000000e+00
#> 207 Enterobacter Male 5 4.035776e-03
#> 208 Escherichia Male 5 0.000000e+00
#> 209 Haemophilus Male 5 1.645411e-02
#> 210 Kocuria Male 5 9.284262e-02
#> 211 Listeria Male 5 8.081554e-04
#> 212 Moraxella Male 5 1.605611e-02
#> 213 Mycoplasma Male 5 2.431315e-04
#> 214 Noviherbaspirillum Male 5 7.839088e-02
#> 215 Other Male 5 5.470460e-03
#> 216 Paracoccus Male 5 5.310659e-04
#> 217 Pseudomonas Male 5 1.962648e-02
#> 218 Staphylococcus Male 5 1.656998e-01
#> 219 Streptococcus Male 5 2.097397e-02
#> 220 Weissella Male 5 9.533558e-03