dimred: Perform simple dimensionality reduction

In dyndimred: Dimensionality Reduction Methods in a Common Format

Description

Perform simple dimensionality reduction

Usage

dimred(x, method, ndim, ...)

dimred_dm_destiny(
  x,
  ndim = 2,
  distance_method = c("euclidean", "spearman", "cosine")
)

dimred_dm_diffusionmap(
  x,
  ndim = 2,
  distance_method = c("pearson", "spearman", "cosine", "euclidean", "chisquared",
    "hamming", "kullback", "manhattan", "maximum", "canberra", "minkowski")
)

dimred_ica(x, ndim = 3)

dimred_knn_fr(
  x,
  ndim = 2,
  lmds_components = 10,
  distance_method = c("pearson", "spearman", "cosine", "euclidean", "chisquared",
    "hamming", "kullback", "manhattan", "maximum", "canberra", "minkowski"),
  n_neighbors = 10
)

dimred_landmark_mds(
  x,
  ndim = 2,
  distance_method = c("pearson", "spearman", "cosine", "euclidean", "chisquared",
    "hamming", "kullback", "manhattan", "maximum", "canberra", "minkowski")
)

dimred_lle(x, ndim = 3)

dimred_mds(
  x,
  ndim = 2,
  distance_method = c("pearson", "spearman", "cosine", "euclidean", "chisquared",
    "hamming", "kullback", "manhattan", "maximum", "canberra", "minkowski")
)

dimred_mds_isomds(
  x,
  ndim = 2,
  distance_method = c("pearson", "spearman", "cosine", "euclidean", "chisquared",
    "hamming", "kullback", "manhattan", "maximum", "canberra", "minkowski")
)

dimred_mds_sammon(
  x,
  ndim = 2,
  distance_method = c("pearson", "spearman", "cosine", "euclidean", "chisquared",
    "hamming", "kullback", "manhattan", "maximum", "canberra", "minkowski")
)

dimred_mds_smacof(
  x,
  ndim = 2,
  distance_method = c("pearson", "spearman", "cosine", "euclidean", "chisquared",
    "hamming", "kullback", "manhattan", "maximum", "canberra", "minkowski")
)

dimred_pca(x, ndim = 2)

list_dimred_methods()

Arguments

x	Log transformed expression data, with rows as cells and columns as features
method	The name of the dimensionality reduction method to use
ndim	The number of dimensions
...	Any arguments to be passed to the dimensionality reduction method
distance_method	The name of the distance metric, see dynutils::calculate_distance
lmds_components	The number of lmds components to use. If NULL, LMDS will not be performed first. If this is a matrix, it is assumed it is a dimred for x.
n_neighbors	The size of local neighborhood (in terms of number of neighboring sample points).

Examples

library(Matrix)
x <- abs(Matrix::rsparsematrix(100, 100, .5))
dimred(x, "pca", ndim = 3)
dimred(x, "ica", ndim = 3)

if (interactive()) {
  dimred_dm_destiny(x)
  dimred_dm_diffusionmap(x)
  dimred_ica(x)
  dimred_landmark_mds(x)
  dimred_lle(x)
  dimred_mds(x)
  dimred_mds_isomds(x)
  dimred_mds_sammon(x)
  dimred_mds_smacof(x)
  dimred_pca(x)
  dimred_tsne(x)
  dimred_umap(x)
}

dyndimred documentation built on March 23, 2021, 9:06 a.m.