QueryStarPlot: QueryStarPlot

View source: R/5_plotFunctions.R

QueryStarPlotR Documentation

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"))
   

SofieVG/FlowSOM documentation built on Feb. 1, 2024, 11:33 a.m.