QueryStarPlot {FlowSOM} | R Documentation |
Query a certain cell type
QueryStarPlot( fsom, query, plot = TRUE, colorPalette = FlowSOM_colors, backgroundColors = "#CA0020", ... )
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. |
colorPalette |
ColorPalette 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 |
Identify nodes in the tree which resemble a certain profile of "high" or "low" marker expressions.
A list, containing the ids of the selected nodes, the individual scores for all nodes and the scores for each marker for each node
PlotStars
, PlotVariable
,
PlotFlowSOM
, PlotLabels
,
PlotNumbers
, PlotMarker
,
PlotPies
, PlotSD
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"))