runTsne: runTsne

In EngeLab/CIMseq: CIMseq is a software suite for analysis of scRNAseq data that has been produced using the cellular interactions by multiplet sequencing method

Description

Calculates the x and y coordinates of the mean of each classif ied group.

Usage

runTsne(
  my.dist,
  dims = 2,
  theta = 0,
  initial_dims = 50,
  max_iter = 2000,
  perplexity = 10,
  seed = 11,
  is_distance = TRUE,
  ...
)

Arguments

my.dist	A distance object typically produced with pearsonsDist.
dims	Argument to Rtsne. Numeric indicating the output dimensions.
theta	Argument to [Rtsne](https://cran.r-project.org/web/packages/Rtsne/index.html).
initial_dims	Argument to [Rtsne](https://cran.r-project.org/web/packages/Rtsne/index.html).
max_iter	Argument to [Rtsne](https://cran.r-project.org/web/packages/Rtsne/index.html).
perplexity	Argument to [Rtsne](https://cran.r-project.org/web/packages/Rtsne/index.html).
seed	The desired seed to set before running.
is_distance	Argument to [Rtsne](https://cran.r-project.org/web/packages/Rtsne/index.html).
...	Additional arguments to pass on

Details

This method is typically only used in conjunction with plotting. It calculates the 2 dimensional location of the mean of each classified group in the supplied unsupervised dimensionality reduction (t-SNE) data representation.

Value

A matrix containing the mean value for each gene for each classification group.

Author(s)

Jason T. Serviss

Examples

my.dist <- pearsonsDist(getData(CIMseqSinglets_test, "counts.cpm"), 1:2000)
tsne <- runTsne(my.dist, max_iter = 10)

EngeLab/CIMseq documentation built on Jan. 25, 2022, 5 a.m.