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, ...) ## S4 method for signature 'daFrame' plotCodes(x, k = "meta20", out_path = NULL, verbose = TRUE)
x |
a |
... |
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. |
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)
data(PBMC_fs, PBMC_panel, PBMC_md) re <- daFrame(PBMC_fs, PBMC_panel, PBMC_md) # run clustering re <- cluster(re) plotCodes(re)