cytof_dimReduction: Dimension reduction for high dimension data

In JinmiaoChenLab/cytofkit2: cytofkit2: an integrated mass cytometry data analysis pipeline. Cytofkit provides functions for data pre-processing, fast clustering, data visualization through linear or non-linear dimensionality reduction, automatic identification of cell subsets, and inference of the relatedness between cell subsets

Dimension reduction for high dimension data

Description

Apply dimension reduction on the cytof expression data, with method pca, tsne, umap or isomap.

Usage

cytof_dimReduction(
  data,
  markers = NULL,
  method = c("umap", "tsne", "pca", "isomap", "NULL"),
  distMethod = "euclidean",
  out_dim = 2,
  umap_neighbor = 30,
  umap_min_dist = 0.3,
  tsneSeed = 42,
  isomap_k = 5,
  isomap_ndim = NULL,
  isomapFragmentOK = TRUE,
  ...
)

Arguments

data	Input expression data matrix.
markers	Selected markers for dimension reduction, either marker names/descriptions or marker IDs.
method	Method chosen for dimensition reduction, must be one of isomap, pca , or tsne.
distMethod	Method for distance calcualtion, default is "euclidean", other choices like "manhattan", "cosine", "rankcor"....
out_dim	The dimensionality of the output.
umap_neighbor	This parameter controls how UMAP balances local versus global structure in the data.
umap_min_dist	Controls how tightly UMAP is allowed to pack points together.
tsneSeed	Set a seed if you want reproducible t-SNE results.
isomap_k	Number of shortest dissimilarities retained for a point, parameter for isomap method.
isomap_ndim	Number of axes in metric scaling, parameter for isomap method.
isomapFragmentOK	What to do if dissimilarity matrix is fragmented, parameter for isomap method.
...	Other parameters passed to the method, check Rtsne, umap, isomap.

Value

A matrix of the dimension reduced data, with colnames method_ID, and rownames same as the input data.

Examples

data(iris)
in_data <- iris[, 1:4]
markers <- colnames(in_data[, 1:4])
out_data <- cytof_dimReduction(in_data, markers = markers, method = "tsne")

JinmiaoChenLab/cytofkit2 documentation built on May 12, 2022, 8:09 a.m.