AddAnnotation: AddAnnotation

In SofieVG/FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

AddAnnotation

Description

Add annotation to a FlowSOM plot

Usage

AddAnnotation(
  p,
  fsom,
  toAnnotate = NULL,
  prefix = list(metaclusters = "MCL ", clusters = "CL "),
  ...
)

Arguments

p	Plot to add annotation to. When using PlotStars, please use list_insteadof_ggarrange = TRUE.
fsom	FlowSOM object that goes with the plot.
toAnnotate	A named list with "metaclusters" and/or "clusters" as names and a vector with the (meta)clusters that need to be annotated. Names can be abbreviated. Use a named vector with the old names as values and new labels as names for custom labeling.
prefix	Prefix to be added to labels. Default is "MCL " and "CL " for metaclusters and clusters respectively.
...	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)
annotationList <- list("metaclusters" = c("CD8 T cells" = "1", "B cells" = "8"),
                   "clusters" = c(97))
AddAnnotation(p, flowSOM.res, toAnnotate = annotationList, 
              prefix = list("metaclusters" = "", clusters = "CL "))

SofieVG/FlowSOM documentation built on Feb. 1, 2024, 11:33 a.m.