tSNE {CATALYST}R Documentation

Run t-SNE

Description

Runs t-SNE dimensionality reduction on a daFrame.

Usage

tSNE(x, ...)

## S4 method for signature 'daFrame'
tSNE(x, cols_to_use = NULL, n = 1000, verbose = TRUE,
  seed = 42)

Arguments

x

a daFrame.

...

optional arguments.

cols_to_use

a character vector. Specifies which antigens to use for clustering. If NULL, the function will attempt to use the type_markers(x).

n

numeric. Specifies the number of cells to downsample to per sample.

verbose

logical. Should information on progress be reported?

seed

numeric. Specifies the seed to be set before sampling

Value

Writes the tSNE coordinates and the indicies of the events used for their computation into the metadata slot of the input daFrame.

Author(s)

Helena Lucia Crowell crowellh@student.ethz.ch

References

Nowicka M, Krieg C, Weber LM et al. CyTOF workflow: Differential discovery in high-throughput high-dimensional cytometry datasets. F1000Research 2017, 6:748 (doi: 10.12688/f1000research.11622.1)

See Also

plotSNE

Examples

# construct daFrame
data(PBMC_fs, PBMC_panel, PBMC_md)
re <- daFrame(PBMC_fs, PBMC_panel, PBMC_md)

# run t-SNE
lineage <- c("CD3", "CD45", "CD4", "CD20", "CD33", 
    "CD123", "CD14", "IgM", "HLA_DR", "CD7")
re <- tSNE(re, cols_to_use=lineage, n=50)

par(pty="s")
tsne <- S4Vectors::metadata(re)$tsne$Y
plot(tsne, pch=20)


[Package CATALYST version 1.4.2 Index]