| dimred_umap {animalcules} | R Documentation |
Dimensionality reduction through PCA
dimred_umap(
MAE,
tax_level,
color,
shape = NULL,
cx = 1,
cy = 2,
cz = NULL,
n_neighbors = 15,
metric = c("euclidean", "manhattan"),
n_epochs = 200,
init = c("spectral", "random"),
min_dist = 0.1,
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" |
cx |
Component on the x-axis e.g. 1 |
cy |
Component on the y-axis e.g. 2 |
cz |
Component on the z-axis e.g. 3 |
n_neighbors |
Number of nearest neighbors |
metric |
Distance function e.g. c("euclidean", "manhattan") |
n_epochs |
Number of iterations |
init |
Initial embedding using eigenvector e.g c("spectral", "random") |
min_dist |
Determines how close points appear in the final layout |
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_umap(toy_data,
tax_level="genus",
color="AGE",
shape="DISEASE",
cx=1,
cy=2,
datatype="logcpm")
result$plot