comptsne: Computation of a two dimensional t-SNE representation

In RaceID: Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Computation of a two dimensional t-SNE representation

Description

This functions performs the computation of a t-SNE map from the distance object in slot distances using the Rtsne package.

Usage

comptsne(
  object,
  dimRed = FALSE,
  initial_cmd = TRUE,
  perplexity = 30,
  rseed = 15555
)

Arguments

object	SCseq class object.
dimRed	logical. If TRUE then the t-SNE is computed from the feature matrix in slot dimRed$x (if not equal to NULL). Default is FALSE and the t-SNE is computed from the distance matrix stored in slot distances. If slot distances equals NULL dimRed is automatially set to TRUE.
initial_cmd	logical. If TRUE, then the t-SNE map computation is initialized with a configuration obtained by classical multidimensional scaling. Default is TRUE.
perplexity	Positive number. Perplexity of the t-SNE map. Default is 30.
rseed	Integer number. Random seed to enforce reproducible t-SNE map.

Value

SCseq object with t-SNE coordinates stored in slot tsne.

Examples

sc <- SCseq(intestinalDataSmall)
sc <- filterdata(sc)
sc <- compdist(sc)
sc <- clustexp(sc)
sc <- findoutliers(sc)
sc <- comptsne(sc)

RaceID documentation built on Sept. 28, 2023, 5:06 p.m.