PlotManualBars {FlowSOM}R Documentation

PlotManualBars

Description

Function to plot the manual labels per FlowSOM (meta)cluster in a barplot

Usage

PlotManualBars(
  fsom,
  fcs = NULL,
  manualVector,
  manualOrder = NULL,
  colors = NULL,
  list_insteadof_plots = FALSE
)

Arguments

fsom

FlowSOM object, as generated by FlowSOM or by NewData.

fcs

Fcs file that should be mapped on the FlowSOM object. Default is NULL.

manualVector

Vector with cell labels, e.g. obtained by manual gating

manualOrder

Optional vector with unique cell labels to fix in which order the cell labels should be shown

colors

Optional color vector, should have the same length as the number of unque cell labels

list_insteadof_plots

If FALSE (default), it returns multiple plots. If TRUE, it returns a list of ggplot objects

Value

Either a plot or a ggplot objects list is returned.

Examples

# Identify the files
fcs_file <- system.file("extdata", "68983.fcs", package = "FlowSOM")
wsp_file <- system.file("extdata", "gating.wsp", package = "FlowSOM")

# Specify the cell types of interest for assigning one label per cell
cellTypes <- c("B cells",
                "gd T cells", "CD4 T cells", "CD8 T cells",
                "NK cells", "NK T cells")
                
# Parse the FlowJo workspace   
library(flowWorkspace)             
gatingResult <- GetFlowJoLabels(fcs_file, wsp_file,
                                cellTypes = cellTypes)               

# Build a FlowSOM object
flowSOM.res <- FlowSOM(fcs_file,
                       scale = TRUE,
                       compensate = TRUE, 
                       transform = TRUE,
                       toTransform = 8:18, 
                       colsToUse = c(9, 12, 14:18),
                       nClus = 10,
                       seed = 1)

# Make the barplot of the manual labels
pdf("PlotManualBars.pdf")
PlotManualBars(fsom = flowSOM.res,
               fcs = fcs_file,
               manualVector = gatingResult$manual,
               manualOrder = c(cellTypes, "Unlabeled"),
               colors = c("#F8766D", "#B79F00", "#00BA38", "#00BFC4", 
                          "#619CFF", "#F564E3", "#D3D3D3"))
dev.off()
[Package FlowSOM version 2.0.0 Index]