BoxPlotMarkerMetaClust: Box plot of one marker MFI, for the different meta-cluster...
In gautierstoll/CytoSOM: Easy use of FlowSOM

Description Usage Arguments Value Examples

BoxPlotMarkerMetaClust is a function that compares, inside each metacluster, the median fluorescence intensity of one given marker for each experimental condition.

BoxPlotMarkerMetaClust(
  TreeMetaCl,
  Title,
  treatmentTable,
  ControlTreatment,
  BottomMargin,
  Marker,
  Robust = TRUE,
  ClustHeat = TRUE
)

`TreeMetaCl`	FlowSOM tree with meta-clusters, constructed by buildFSOMTree
`Title`	prefix of the pdf file name
`treatmentTable`	data frame containing a column 'files' and a column 'Treatment' (case sensitive)
`BottomMargin`	size of the boxplots bottom margins, in order to be readable
`Marker`	marker name
`Robust`	if TRUE, robust statistics is applied (dunn), otherwise linear-model/Tukey
`ClustHeat`	if TRUE, heatmaps are clustered
`Controltreatment`	name of the experimental condition that you consider as your control treatment used for statistics

list containing MFI, pairwise comparison p-values, controle vs treatment p-values

1	BoxPlotMarkerMetaClust(TreeMetaCl=CytoTree, Title="Experiment1",treatmentTable=Experiment1table.csv,ControlTreatment="control",BottomMargin=3,Marker="PD-1",Robust=TRUE, ClustHeat=TRUE)