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]