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 1.8.5 Index]