plotSNE {CATALYST} | R Documentation

## plot t-SNE

### Description

t-SNE plot colored by marker expression or clustering.

### Usage

    plotSNE(x, ...)

    ## S4 method for signature 'daFrame'
    plotSNE(x, color_by = 20, facet = NULL)

### Arguments

`x` | a `daFrame`.
`...` | optional arguments.
`color_by` | numeric value or character string specifying a clustering OR a character string specifying an antibody whose expression to color by.
`facet` | a character string specifying a factor to subset the data by. One of `names(rowData(x))`. Defaults to NULL.

### Value

a `ggplot` object.

### 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)

### Examples

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

    # run clustering
    lineage <- c("CD3", "CD45", "CD4", "CD20", "CD33",
        "CD123", "CD14", "IgM", "HLA_DR", "CD7")
    re <- cluster(re, cols_to_use=lineage)

    # run t-SNE
    re <- tSNE(re, n=50)

    # color by clustering
    plotSNE(re, color_by=12)

    # color by marker expression
    plotSNE(re, color_by="pNFkB", facet="condition")

[Package CATALYST version 1.4.2 Index]