GetClusterPercentagesPositive: Get percentage-positive values for all clusters

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

Get percentage-positive values for all clusters

Description

Get percentage-positive values for all clusters

Usage

GetClusterPercentagesPositive(
  fsom,
  cutoffs,
  colsUsed = FALSE,
  prettyColnames = FALSE
)

Arguments

fsom	FlowSOM object as generated by the FlowSOM function or the BuildSOM function
cutoffs	named numeric vector. Upper bounds of negative population fluorescence-intensity values for each marker / channel.
colsUsed	logical. Should report only the columns used to build the SOM. Default = FALSE.
prettyColnames	logical. Should report pretty column names instead of standard column names. Default = FALSE.

Value

Matrix with percentages of cells that are positive in selected markers per each cluster

Examples

fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM")
flowSOM.res <- FlowSOM(fileName, compensate = TRUE, transform = TRUE,
                      scale = TRUE, colsToUse = c(9, 12, 14:18), nClus = 10)
perc_pos <- GetClusterPercentagesPositive(flowSOM.res, cutoffs = c('CD4' = 5000))

saeyslab/FlowSOM documentation built on July 6, 2024, 10:59 a.m.