fftRtsne: Wraper for running FIt-SNE. Code from KlugerLab...
In Japrin/sscClust: simpler single cell RNAseq data clustering

fftRtsne

R Documentation

Wraper for running FIt-SNE. Code from KlugerLab (https://github.com/KlugerLab/FIt-SNE)

Description

Wraper for running FIt-SNE. Code from KlugerLab (https://github.com/KlugerLab/FIt-SNE)

Usage

fftRtsne(
  X,
  dims = 2,
  perplexity = 30,
  theta = 0.5,
  max_iter = 1000,
  fft_not_bh = TRUE,
  ann_not_vptree = TRUE,
  stop_early_exag_iter = 250,
  exaggeration_factor = 12,
  no_momentum_during_exag = FALSE,
  start_late_exag_iter = -1,
  late_exag_coeff = 1,
  mom_switch_iter = 250,
  momentum = 0.5,
  final_momentum = 0.8,
  learning_rate = 200,
  n_trees = 50,
  search_k = -1,
  rand_seed = -1,
  nterms = 3,
  intervals_per_integer = 1,
  min_num_intervals = 50,
  K = -1,
  sigma = -30,
  initialization = NULL,
  data_path = NULL,
  result_path = NULL,
  out_prefix = NULL,
  load_affinities = NULL,
  fast_tsne_path = NULL,
  nthreads = 0,
  perplexity_list = NULL,
  get_costs = FALSE,
  df = 1
)

Arguments

`X`	matrix; samples in rows and variables in columns
`dims`	integer; dimentionality of the returned matrix
`perplexity`	double; perplexity parameter of tSNE (effective nearest neighbours)
`theta`	double; theta
`max_iter`	integer; max_iter
`fft_not_bh`	logical; fft_not_bh (default: TRUE)
`ann_not_vptree`	logical; (default: TRUE)
`stop_early_exag_iter`	integer; (default 250)
`exaggeration_factor`	double;
`no_momentum_during_exag`	logical;
`start_late_exag_iter`	double;
`late_exag_coeff`	double;
`mom_switch_iter`	double;
`momentum`	double;
`final_momentum`	double;
`learning_rate`	double;
`n_trees`	integer;
`search_k`	double;
`rand_seed`	double;
`nterms`	integer;
`intervals_per_integer`	integer;
`min_num_intervals`	integer;
`K`	integer;
`sigma`	double;
`initialization`	matrix
`data_path`	character;
`result_path`	character;
`out_prefix`	character; temporary files prefix for fast_tsne (default: NULL)
`load_affinities`	character;
`fast_tsne_path`	character; full path of the installed fast_tsne programe (default: NULL)
`nthreads`	integer; number of threads (default: 0)
`perplexity_list`	list;
`get_costs`	logical;
`df`	numeric;