destiny-deprecated: Compatibility versions of functions for destiny 1.x scripts

Description

This is most useful if you have old scripts that use the old argument order and the default being global sigma. Simply put DiffusionMap <- DiffusionMapCompat on top of your script to make it work with destiny 2.x.

Usage

DiffusionMapCompat(data, sigma = "global", k = find_dm_k(nrow(data) - 1L),
  n.eigs = min(20L, nrow(data) - 2L), density.norm = TRUE, ...,
  distance = c("euclidean", "cosine", "rankcor"), censor.val = NULL,
  censor.range = NULL, missing.range = NULL, vars = NULL,
  verbose = !is.null(censor.range))
cube.helix(n = 6, start = 0, r = 0.4, hue = 0.8, gamma = 1,
  light = 0.85, dark = 0.15, reverse = FALSE)
dm.predict(dm, new.data, verbose = FALSE)
eig.decomp(M, n.eigs, sym = isSymmetric(M))
find.dm.k(n, min.k = 100L, small = 1000L, big = 10000L)
find.sigmas(data, step.size = 0.1, steps = 10L, start = NULL,
  sample.rows = 500L, early.exit = FALSE, ..., censor.val = NULL,
  censor.range = NULL, missing.range = NULL, vars = NULL,
  verbose = TRUE)
optimal.sigma(object)
lWhich(idx, nms = seq_len(len), len = length(nms), useNames = TRUE)

Arguments

data, n, n.eigs, start, censor.val, censor.range, missing.range, vars, verbose, ...

Corresponding parameters in multiple functions

sigma, k, density.norm, distance

Corresponding DiffusionMap parameters

r, hue, gamma, light, dark, reverse

Corresponding cube_helix parameters

dm, new.data

Corresponding dm_predict parameters

M, sym

Corresponding eig_decomp parameters

min.k, small, big

Corresponding find_dm_k parameters

step.size, steps, sample.rows, early.exit

Corresponding find_sigmas parameters

object

Corresponding optimal_sigma parameters