Dimensionality reduction through PCoA
dimred_pcoa(
MAE,
tax_level,
color,
shape = NULL,
axx = 1,
axy = 2,
axz = NULL,
method = c("bray", "jaccard")
)A multi-assay experiment object
The taxon level used for organisms
A condition to color data points by e.g. "AGE"
A condition to shape data points by e.g. "SEX"
Principle coordinate on the x-axis e.g. 1
Principle coordinate on the y-axis e.g. 2
Principle coordinate on the z-axis e.g. 2
Method to use e.g. c("bray", "jaccard")
A list with a plotly object and summary table
data_dir <- system.file("extdata/MAE.rds", package = "animalcules")
toy_data <- readRDS(data_dir)
result <- dimred_pcoa(toy_data,
tax_level = "genus",
color = "AGE",
shape = "DISEASE",
axx = 1,
axy = 2,
method = "bray"
)
result$plot
result$table
#> Axis Eigenvalue Variance Explained Cumulative Variance
#> Axis.1 Axis.1 3.64000 19.6142% 19.61%
#> Axis.2 Axis.2 2.86000 15.5122% 35.13%
#> Axis.3 Axis.3 1.72000 9.5218% 44.65%
#> Axis.4 Axis.4 0.86100 5.0201% 49.67%
#> Axis.5 Axis.5 0.84600 4.9398% 54.61%
#> Axis.6 Axis.6 0.70900 4.2222% 58.83%
#> Axis.7 Axis.7 0.54700 3.3659% 62.20%
#> Axis.8 Axis.8 0.46200 2.9214% 65.12%
#> Axis.9 Axis.9 0.44700 2.8404% 67.96%
#> Axis.10 Axis.10 0.37200 2.4476% 70.41%
#> Axis.11 Axis.11 0.35600 2.3656% 72.77%
#> Axis.12 Axis.12 0.29200 2.0247% 74.80%
#> Axis.13 Axis.13 0.26300 1.8742% 76.67%
#> Axis.14 Axis.14 0.22100 1.6526% 78.32%
#> Axis.15 Axis.15 0.20900 1.5909% 79.91%
#> Axis.16 Axis.16 0.18300 1.4556% 81.37%
#> Axis.17 Axis.17 0.15800 1.3222% 82.69%
#> Axis.18 Axis.18 0.11800 1.1105% 83.80%
#> Axis.19 Axis.19 0.10200 1.0283% 84.83%
#> Axis.20 Axis.20 0.09600 0.9958% 85.83%
#> Axis.21 Axis.21 0.08950 0.9619% 86.79%
#> Axis.22 Axis.22 0.06490 0.8323% 87.62%
#> Axis.23 Axis.23 0.05360 0.7731% 88.39%
#> Axis.24 Axis.24 0.05060 0.7572% 89.15%
#> Axis.25 Axis.25 0.04230 0.7133% 89.86%
#> Axis.26 Axis.26 0.03470 0.6733% 90.54%
#> Axis.27 Axis.27 0.03200 0.6591% 91.20%
#> Axis.28 Axis.28 0.02380 0.6159% 91.81%
#> Axis.29 Axis.29 0.01850 0.5881% 92.40%
#> Axis.30 Axis.30 0.01400 0.5648% 92.97%
#> Axis.31 Axis.31 0.00684 0.5270% 93.49%
#> Axis.32 Axis.32 0.00553 0.5201% 94.01%
#> Axis.33 Axis.33 0.00363 0.5101% 94.52%
#> Axis.34 Axis.34 0.00242 0.5038% 95.03%
#> Axis.35 Axis.35 0.00000 0.4892% 95.52%
#> Axis.36 Axis.36 -0.00034 0.4760% 95.99%
#> Axis.37 Axis.37 -0.00286 0.4452% 96.44%
#> Axis.38 Axis.38 -0.00871 0.4435% 96.88%
#> Axis.39 Axis.39 -0.00904 0.4244% 97.30%
#> Axis.40 Axis.40 -0.01270 0.3910% 97.70%
#> Axis.41 Axis.41 -0.01900 0.3734% 98.07%
#> Axis.42 Axis.42 -0.02240 0.3538% 98.42%
#> Axis.43 Axis.43 -0.02610 0.3267% 98.75%
#> Axis.44 Axis.44 -0.03120 0.2905% 99.04%
#> Axis.45 Axis.45 -0.03810 0.2716% 99.31%
#> Axis.46 Axis.46 -0.04170 0.2553% 99.57%
#> Axis.47 Axis.47 -0.04480 0.2373% 99.80%
#> Axis.48 Axis.48 -0.04820 0.1962% 100.00%
#> Axis.49 Axis.49 -0.05610 0.0000% 100.00%
#> Axis.50 Axis.50 -0.09340 0.0000% 100.00%