celda (version 0.0.0.9000)

celdaTsne: Runs tSNE via Rtsne based on the CELDA model and specified cell states.

Description

Runs tSNE via Rtsne based on the CELDA model and specified cell states.

Usage

celdaTsne(counts, celda.mod, states = NULL, perplexity = 20,
  max.iter = 2500, distance = "hellinger")

Arguments

counts

Counts matrix, will have cell name for column name and gene name for row name.

celda.mod

Celda model to use for tsne. class "celda_C","celda_G" or "celda_CG".

states

Vector; determines which cell states to use for tsne. If not defined, all states will be used.

perplexity

Numeric vector; determines perplexity for tsne. Default 20.

max.iter

Numeric vector; determines iterations for tsne. Default 1000.

distance

Character vector; determines which distance metric to use for tsne. Options: cosine, hellinger, spearman.