QueryStarPlot: QueryStarPlot

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

QueryStarPlot

Description

Query a certain cell type

Usage

QueryStarPlot(
  fsom,
  query,
  plot = TRUE,
  colorPalette = FlowSOM_colors,
  backgroundColors = "#CA0020",
  ...
)

Arguments

fsom	FlowSOM object, as generated by BuildMST
query	Array containing "high" or "low" (or abbreviations) for the specified column names of the FlowSOM data.
plot	If true, a plot with a gradient of scores for the nodes is shown.
colorPalette	Color palette to be used for colors for "stars", "pies" or "marker". Can be either a function or an array specifying colors.
backgroundColors	Color to use for nodes with a high score in the plot. Default is red.
...	Additional arguments to pass to PlotFlowSOM

Details

Identify nodes in the tree which resemble a certain profile of "high" or "low" marker expressions.

Value

A list, containing the ids of the selected nodes, the individual scores for all nodes and the scores for each marker for each node

See Also

PlotStars, PlotVariable, PlotFlowSOM, PlotLabels, PlotNumbers, PlotMarker, PlotPies, PlotSD

Examples

   file <- system.file("extdata", "68983.fcs", package="FlowSOM")
   flowSOM.res <- FlowSOM(file, compensate = TRUE, transform = TRUE, 
                  scale = TRUE, colsToUse = c(9, 12, 14:18), nClus = 10, 
                  silent = FALSE, xdim = 7, ydim = 7)
   query <- c("CD3" = "high", #CD3
              "CD4" = "low", #TCRb
              "CD8" = "high") #CD8
   query_res <- QueryStarPlot(flowSOM.res, query, equalNodeSize = TRUE)
   
   cellTypes <- factor(rep("Unlabeled", 49), 
                       levels = c("Unlabeled", "CD8 T cells"))
   cellTypes[query_res$selected] <- "CD8 T cells"
   PlotStars(flowSOM.res,
             backgroundValues = cellTypes,
             backgroundColors = c("#FFFFFF00", "#ca0020aa"))
   

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