FlowSOM (version 1.0.0)

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, tresh=0.5, p_tresh=NULL,...)

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 t-test before the node is coloured. If this is not NULL, tresh will be ignored.

...

Other parameters to pass to PlotStars

Value

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)