destiny-deprecated {destiny} | R Documentation

## 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)

    plot_gradient_map(coords, exprs, ..., gene, dims = 1:2,
      pal = hcl.colors, faceter = facet_wrap(~Gene))

### 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

### Examples

    DiffusionMap <- DiffusionMapCompat
    ## Not run: source('my-old-script.r')

[Package destiny version 3.1.0 Index]