plotCodes {CATALYST} | R Documentation

## tSNE and PCA on SOM codes

### Description

Plots the tSNE and PCA representing the SOM codes as inferred by FlowSOM. Sizes are scaled to the total number of events assigned to each cluster, and points are color according to their cluster ID upon ConsensusClusterPlus metaclustering into `k` clusters.

### Usage

    plotCodes(x, ...)

    ## S4 method for signature 'daFrame'
    plotCodes(x, k = "meta20", out_path = NULL,
      verbose = TRUE)

### Arguments

`x` | a `daFrame`.
`...` | optional arguments.
`k` | character string. Specifies the clustering to use for color coding.
`out_path` | character string. If specified, output will be generated in this location.
`verbose` | logical. Specifies whether information on progress should be reported.

### Value

a `ggplot` object.

### Author(s)

Helena Lucia Crowell helena.crowell@uzh.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

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

    # run clustering
    re <- cluster(re)
    plotCodes(re)

[Package CATALYST version 1.8.7 Index]