quickUmap: run umap on PCA or other dm space

In huqiwen0313/snarePip: snarePip

run umap on PCA or other dm space

Description

run umap on PCA or other dm space

Usage

quickUmap(
  obj,
  space = "PCA",
  dims = NULL,
  n.neighbors = 30L,
  n.components = 2L,
  metric = "cosine",
  n.epochs = NULL,
  learning.rate = 1,
  min.dist = 0.3,
  spread = 1,
  set.op.mix.ratio = 1,
  local.connectivity = 1L,
  repulsion.strength = 1,
  negative.sample.rate = 5,
  a = NULL,
  b = NULL,
  uwot.sgd = FALSE,
  seed.use = 22,
  metric.kwds = NULL,
  angular.rp.forest = FALSE,
  verbose = TRUE
)

Arguments

obj	pagoda object
dims	number of significant PCs for reduction (e.g. 1:20)

huqiwen0313/snarePip documentation built on June 11, 2022, 5:34 p.m.