dimred_pcoa {animalcules} | R Documentation |
Dimensionality reduction through PCoA
dimred_pcoa( MAE, tax_level, color, shape = NULL, axx = 1, axy = 2, axz = NULL, method = c("bray", "jaccard") )
MAE |
A multi-assay experiment object |
tax_level |
The taxon level used for organisms |
color |
A condition to color data points by e.g. "AGE" |
shape |
A condition to shape data points by e.g. "SEX" |
axx |
Principle coordinate on the x-axis e.g. 1 |
axy |
Principle coordinate on the y-axis e.g. 2 |
axz |
Principle coordinate on the z-axis e.g. 2 |
method |
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