PlotManualBars {FlowSOM} | R Documentation |
Function to plot the manual labels per FlowSOM (meta)cluster in a barplot
PlotManualBars( fsom, fcs = NULL, manualVector, manualOrder = NULL, colors = NULL, list_insteadof_plots = FALSE )
fsom |
FlowSOM object, as generated by |
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 |
Either a plot or a ggplot objects list is returned.
# 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()