QueryStarPlot: Query a certain cell type

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

Description

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

Usage

QueryStarPlot(fsom, query, plot = TRUE, color = "#ca0020", debug = FALSE, ...)

Arguments

fsom	FlowSOM object, as generated by BuildMST or the first list item of FlowSOM
query	Array containing "high" or "low" for the specified column names of the FlowSOM data
plot	If true, a plot with a gradient of scores for the nodes is shown
color	Color to use for nodes with a high score in the plot
debug	If TRUE, some extra output will be printed
...	Other parameters to pass to PlotStars

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

Examples

   file <- system.file("extdata", "68983.fcs", package="FlowSOM")
   # Use the wrapper function to build a flowSOM object (saved in fsom[[1]])
   # and a metaclustering (saved in fsom[[2]])
   fsom <- FlowSOM(file,compensate = TRUE, transform = TRUE,scale = TRUE,
                  colsToUse = c(9,12,14:18), nClus = 10, silent = FALSE,
                  xdim=7, ydim=7)
   query <- c("PE-Cy7-A" = "high", #CD3
              "APC-Cy7-A" = "high", #TCRb
              "Pacific Blue-A" = "high") #CD8
   query_res <- QueryStarPlot(UpdateNodeSize(fsom[[1]],reset=TRUE), query)
   
   cellTypes <- factor(rep("Unknown",49),levels=c("Unknown","CD8 T cells"))
   cellTypes[query_res$selected] <- "CD8 T cells"
   PlotStars(fsom[[1]],
                 backgroundValues=cellTypes,
                 backgroundColor=c("#FFFFFF00","#ca0020aa"))
   

FlowSOM documentation built on Nov. 8, 2020, 6:40 p.m.