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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/compat.r
\name{destiny-deprecated}
\alias{destiny-deprecated}
\alias{DiffusionMapCompat}
\alias{cube.helix}
\alias{dm.predict}
\alias{eig.decomp}
\alias{find.dm.k}
\alias{find.sigmas}
\alias{optimal.sigma}
\alias{lWhich}
\alias{plot_gradient_map}
\title{Compatibility versions of functions for destiny 1.x scripts}
\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{
\item{data, n, n.eigs, start, censor.val, censor.range, missing.range, vars, verbose, ...}{Corresponding parameters in multiple functions}
\item{sigma, k, density.norm, distance}{Corresponding \code{\link{DiffusionMap}} parameters}
\item{r, hue, gamma, light, dark, reverse}{Corresponding \code{\link{cube_helix}} parameters}
\item{dm, new.data}{Corresponding \code{\link{dm_predict}} parameters}
\item{M, sym}{Corresponding \code{\link{eig_decomp}} parameters}
\item{min.k, small, big}{Corresponding \code{\link{find_dm_k}} parameters}
\item{step.size, steps, sample.rows, early.exit}{Corresponding \code{\link{find_sigmas}} parameters}
\item{object}{Corresponding \code{\link{optimal_sigma}} parameters}
}
\description{
This is most useful if you have old scripts that use the old argument order and the default being global sigma.
Simply put \code{DiffusionMap <- DiffusionMapCompat} on top of your script to make it work with destiny 2.x.
}
\examples{
DiffusionMap <- DiffusionMapCompat
\dontrun{source('my-old-script.r')}
}
\keyword{internal}
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