AddAnnotation {FlowSOM}R Documentation

AddAnnotation

Description

Add annotation to a FlowSOM plot

Usage

AddAnnotation(
  p,
  fsom,
  layout = fsom$MST$l,
  cl = NULL,
  mcl = NULL,
  clCustomLabels = NULL,
  mclCustomLabels = NULL,
  hjust = 0.5,
  ...
)

Arguments

p

Plot to add annotation to. When using type = "stars", please use plot = FALSE in PlotFlowSOM.

fsom

FlowSOM object that goes with the plot

layout

Layout to use. Default fsom$MST$l

cl

Clusters to annotate. If cl = "all", all clusters will be annotated

mcl

Metaclusters to annotate. If mcl = "all", all metaclusters will be annotated

clCustomLabels

Cluster labels to use for annotation

mclCustomLabels

Metacluster labels to use for annotation

hjust

Label adjustment. Default = 0.5

...

Arguments passed to geom_text_repel

Value

The updated plot

Examples


#' # Identify the files
fcs <- flowCore::read.FCS(system.file("extdata", "68983.fcs", 
                                      package = "FlowSOM"))
# Build a FlowSOM object
flowSOM.res <- FlowSOM(fcs, 
                       scale = TRUE,
                       compensate = TRUE, 
                       transform = TRUE,
                       toTransform = 8:18, 
                       colsToUse = c(9, 12, 14:18),
                       nClus = 10,
                       seed = 1)
                       
p <- PlotStars(flowSOM.res, backgroundValues = flowSOM.res$metaclustering,
               list_insteadof_ggarrange = TRUE)
AddAnnotation(p, flowSOM.res, cl = c(1, 2), mcl = c(3, 4))


[Package FlowSOM version 2.0.0 Index]