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