Tsne-class: The Tsne class

In ilyessr/conclus: ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion

The Tsne class

Description

S4 class containing the features to plot tSNEs. This constructor is internal and is used by the method generateTSNECoordinates.

Details

Tsne is a vector of principal components (PC) and perplexity that are the parameters necessary to reduce the dimensionality of the data in the the form of a t-distributed stochastic neighbor embedding (t-SNE). For details about perplexities parameter see ‘?Rtsne’.

Slots

name

A 'character' string representing the name of the tSNE coordinates.

pc

A 'numeric' value representing the number of principal components used by CONCLUS to perfom a PCA before calculating the tSNE.

perplexity

A 'numeric' vector. Default: c(30, 40)

coordinates

A 'numeric' matrix that contains the coordinates of one tSNE solution.

Constructor

Tsne(name = "character", pc = "numeric", perplexity = "numeric", coordinates = "matrix")

name: Empty character string or the name of the tSNE.
pc: Empty 'numeric' number of PCs.
perplexity: Empty 'numeric' perplexity values.
coordinates: Empty 'numeric' "matrix" or matrix of coordinates.

Accessors

In the following snippets, x is a Tsne object.

getName(x): Get the name of the tSNE.
getPC(x): Get the PC used.
getPerplexity(x): Get the perplexity used.
getCoordinates(x): Get the matrix of tSNE coordinates.

Subsetting

In the following snippets, x is a Tsne object.

setName(x) <- value: Set the name of the tSNE.
setPC(x) <- value: Set the PC parameter.
setPerplexity(x) <- value: Set the perplexity parameter.
setCoordinates(x) <- value: Set the matrix of tSNE coordinates.

Author(s)

Ilyess Rachedi and Nicolas Descostes

See Also

generateTSNECoordinates

ilyessr/conclus documentation built on April 8, 2022, 1:43 p.m.