PlotGroups {FlowSOM} | R Documentation

## PlotGroups

### Description

Plot differences between groups

### Usage

    PlotGroups(fsom, groups, threshold = NULL, pThreshold = 0.05, ...)

### Arguments

`fsom` | FlowSOM object, as generated by `BuildMST`
`groups` | Groups result as generated by `CountGroups`
`threshold` | Relative difference in groups before the node is coloured
`pThreshold` | Threshold on p-value from wilcox-test before the node is coloured. If this is not NULL, threshold will be ignored.
`...` | Additional arguments to pass to `PlotFlowSOM`

### Details

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

### Value

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

### See Also

`PlotStars`,`PlotVariable`, `PlotFlowSOM`,`PlotLabels`,`PlotNumbers`, `PlotMarker`,`PlotPies`,`QueryStarPlot`, `PlotSD`

### Examples

    #Run FlowSOM
    fileName <-  system.file("extdata", "68983.fcs", package="FlowSOM")
    fsom <- FlowSOM(fileName, compensate = TRUE, transform = TRUE,
                          scale = TRUE, colsToUse = c(9,12,14:18), nClus = 10)

    ff <- flowCore::read.FCS(fileName)
    # Make an additional file without cluster 7 and double amount of cluster 5
    selection <- c(which(GetClusters(fsom) %in% which(fsom$metaclustering != 7)),
                     which(GetClusters(fsom) %in% which(fsom$metaclustering == 5)))
    ff_tmp <- ff[selection,]
    flowCore::write.FCS(ff_tmp, file="ff_tmp.fcs")

    # Compare only the file with the double amount of cluster 10
    features <- GetFeatures(fsom,
                            c(fileName, "ff_tmp.fcs"),
                            level = "clusters",
                            type = "percentages")
    stats <- GroupStats(features$cluster_percentages,
                        groups = list("AllCells" = c(fileName),
                                      "Without_ydTcells" = c("ff_tmp.fcs")))

    fold_changes <- stats["fold changes", ]
    fold_changes_label <- factor(ifelse(fold_changes < -1.5,
                               "Underrepresented compared to Group 1",
                               ifelse(fold_changes > 1.5,
                                      "Overrepresented compared to Group 1",
                                      "--")),
                                levels = c("--",
                                   "Underrepresented compared to Group 1",
                                   "Overrepresented compared to Group 1"))
    fold_changes_label[is.na(fold_changes_label)] <- "--"
    gr_1 <- PlotStars(fsom,
                      title = "All Cells",
                      nodeSizes = stats["medians AllCells", ],
                      list_insteadof_ggarrange = TRUE)
    gr_2 <- PlotStars(fsom, title = "Group 2",
                   nodeSizes = stats["medians Without_ydTcells", ],
                    backgroundValues = fold_changes_label,
                   backgroundColors = c("white", "red", "blue"),
                   list_insteadof_ggarrange = TRUE)
    p <- ggpubr::ggarrange(plotlist = c(list(gr_1$tree), gr_2),
                        heights = c(3, 1))
    p

[Package FlowSOM version 2.2.0 Index]