FlowSOM (version 1.0.0)

CountGroups: Compute differences between groups

Description

Map new data to the flowSOM grid and average over all files from one group

Usage

CountGroups(fsom, groups, plot=TRUE, silent=FALSE)

Arguments

fsom

FlowSOM object, as generated by BuildMST

groups

List with for every group a vector with filepaths

plot

Logical: if TRUE, the star plot is shown for each individual file, with adapted node size

silent

Logical: if FALSE, progress is printed

Value

See Also

PlotStars,PlotGroups,codeNewData

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)