t-SNE ordering — tSNE_ordering • smoothEMr

t-SNE ordering

tSNE_ordering(
  X,
  tSNE_dims = 1,
  component = 1,
  perplexity = 10,
  max_iter = 500,
  seed = NULL,
  scale01 = TRUE,
  orient_by_pc1 = TRUE
)

Arguments

X: numeric matrix (n x D).
tSNE_dims: integer; embedding dimension passed to Rtsne.
component: which embedding coordinate to use as ordering (default 1).
perplexity: t-SNE perplexity; must satisfy < (n-1)/3.
max_iter: max iterations.
seed: optional integer for reproducibility.
scale01: logical; if TRUE, rescale returned t to [0,1].
orient_by_pc1: logical; if TRUE, flip sign to align with PC1.

Value

list(t, keep_idx)