PlotGroups: Plot differences between groups

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

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, tresh = NULL, p_tresh = 0.05, heatmap = FALSE, ...)

Arguments

fsom	FlowSOM object, as generated by BuildMST or the first list item of FlowSOM
groups	groups result as generated by CountGroups
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)
   

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

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