QueryStarPlot {FlowSOM} | R Documentation |
Identify nodes in the tree which resemble a certain profile of "high" or "low" marker expressions.
QueryStarPlot(fsom, query, plot = TRUE, color = "#ca0020", debug = FALSE, ...)
fsom |
FlowSOM object, as generated by |
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 |
A list, containing the ids of the selected nodes, the individual scores for all nodes and the scores for each marker for each node
file <- system.file("extdata","lymphocytes.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"))