dimred_pca {animalcules} | R Documentation |
Dimensionality reduction through PCA
dimred_pca( MAE, tax_level, color, shape = NULL, pcx = 1, pcy = 2, pcz = NULL, datatype = c("logcpm", "relabu", "counts") )
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" |
pcx |
Principal component on the x-axis e.g. 1 |
pcy |
Principal component on the y-axis e.g. 2 |
pcz |
Principal component on the z-axis e.g. 3 |
datatype |
Datatype to use e.g. c("logcpm", "relabu", "counts") |
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_pca(toy_data, tax_level="genus", color="AGE", shape="DISEASE", pcx=1, pcy=2, datatype="logcpm") result$plot result$table