R/compat.r
destiny-deprecated.Rd
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.
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))
data, n, n.eigs, start, censor.val, censor.range, missing.range, vars, verbose, ... | Corresponding parameters in multiple functions |
---|---|
sigma, k, density.norm, distance | Corresponding |
r, hue, gamma, light, dark, reverse | Corresponding |
dm, new.data | Corresponding |
M, sym | Corresponding |
min.k, small, big | Corresponding |
step.size, steps, sample.rows, early.exit | Corresponding |
object | Corresponding |
DiffusionMap <- DiffusionMapCompat# NOT RUN { source('my-old-script.r') # }