FlowSOM (version 1.4.0)

PlotGroups: Plot differences between groups

Description

Plot FlowSOM trees, where each node is represented by a star chart indicating mean marker values, the size of the node is relative to the mean percentage of cells present in each

Usage

PlotGroups(fsom, groups, view = "MST", tresh = 0.5, p_tresh = NULL, heatmap = FALSE, ...)

Arguments

fsom

FlowSOM object, as generated by BuildMST or the first list item of FlowSOM

groups

groups result as generated by CountGroups

view

Preferred view, options: "MST", "grid" or "tSNE" (if this option was selected while building the MST)

tresh

Relative difference in groups before the node is coloured

p_tresh

Threshold on p-value from wilcox-test before the node is coloured. If this is not NULL, tresh will be ignored.

heatmap

If TRUE, the scores are plotted in a gradient instead of only the selection that passes the threshold

...

Other parameters to pass to PlotStars

Value

A vector containing the labels assigned to the nodes for all groups except the first

See Also

PlotStars,CountGroups

Examples

   ## Use the wrapper function to build a flowSOM object (saved in fsom[[1]])
   ## and a metaclustering (saved in fsom[[2]])
   # fsom <- FlowSOM(ff,compensate = FALSE, transform = FALSE,scale = TRUE,
   #              colsToUse = colsToUse, nClus = 10, silent = FALSE,
   #             xdim=7, ydim=7)
   
   ## Make a list with for each group a list of files
   ## The reference group should be the first
   # groups <- list("C"=file.path(workDir,grep("C",files,value = TRUE)),
   #             "D"=file.path(workDir,grep("D",files,value=TRUE)))
   
   ## Compute the percentages for all groups
   # groups_res <- CountGroups(fsom[[1]],groups)
  
   ## Plot the groups. For all groups except the first, differences with the
   ## first group are indicated
   # annotation <- PlotGroups(fsom[[1]],groups_res)