PlotGroups {FlowSOM} | R Documentation

## 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, 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)

[Package FlowSOM version 1.20.0 Index]