PlotGroups {FlowSOM} | R Documentation |
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
PlotGroups(fsom, groups, tresh = NULL, p_tresh = 0.05, heatmap = FALSE, ...)
fsom |
FlowSOM object, as generated by |
groups |
groups result as generated by |
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 |
A vector containing the labels assigned to the nodes for all groups except the first
## 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)