PlotManualBars: PlotManualBars

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

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. The clusters and metaclusters will be plotted in the order of the factor levels.
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 unique 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")
gating_file <- system.file("extdata", "gatingResult.csv", 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")
                
# Load manual labels (e.g. GetFlowJoLabels can be used to extract labels from
# an fcs file)
 
gatingResult <- as.factor(read.csv(gating_file, header = FALSE)[, 1])

# 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,
               manualOrder = c(cellTypes, "Unlabeled"),
               colors = c("#F8766D", "#B79F00", "#00BA38", "#00BFC4", 
                          "#619CFF", "#F564E3", "#D3D3D3"))
dev.off()

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