plotCodes {CATALYST} | R Documentation |
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.
plotCodes(x, k = "meta20", out_path = NULL, verbose = TRUE)
x |
|
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. Should information on progress be reported? |
a ggplot
object.
Helena Lucia Crowell helena.crowell@uzh.ch
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)
# construct SCE & run clustering data(PBMC_fs, PBMC_panel, PBMC_md) sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md) sce <- cluster(sce) plotCodes(sce, k = "meta14")