celdaTsne: Embeds cells in two dimensions using tSNE based on celda_CG...

Description Usage Arguments Value Examples

Description

Embeds cells in two dimensions using tSNE based on celda_CG results.

Usage

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celdaTsne(
  counts,
  celdaMod,
  maxCells = 25000,
  minClusterSize = 100,
  initialDims = 20,
  modules = NULL,
  perplexity = 20,
  maxIter = 2500,
  ...
)

Arguments

counts

Integer matrix. Rows represent features and columns represent cells. This matrix should be the same as the one used to generate 'celdaMod'.

celdaMod

Celda object of class 'celda_CG'.

maxCells

Integer. Maximum number of cells to plot. Cells will be randomly subsampled if ncol(counts) > maxCells. Larger numbers of cells requires more memory. Default 25000.

minClusterSize

Integer. Do not subsample cell clusters below this threshold. Default 100.

initialDims

integer. The number of dimensions that should be retained in the initial PCA step. Default 20.

modules

Integer vector. Determines which features modules to use for tSNE. If NULL, all modules will be used. Default NULL.

perplexity

Numeric. Perplexity parameter for tSNE. Default 20.

maxIter

Integer. Maximum number of iterations in tSNE generation. Default 2500.

...

Additional parameters.

Value

Numeric Matrix of dimension 'ncol(counts)' x 2, colums representing the "X" and "Y" coordinates in the data's t-SNE represetation.

Examples

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celda documentation built on June 9, 2020, 2 a.m.