plotTreeSet: Plot a set of trees, in a pdf file, for metaclusters and...

In gautierstoll/CytoSOM: Easy use of FlowSOM

Description

plotTreeSet is a function that allows the automatic export of

• one PDF file containing the plot of the general tree and its representation according to each experimental condition

• one PDF file containing the representation on the general and treatment specific of the median fluorescent intensity of one choosen marker

the treatmentTable should be a dataframe with two column: "Treatment", "files"

Usage

plotTreeSet(
  TreeMetacl,
  markers,
  Title,
  rmClNb,
  treatmentTable,
  globalScale = T
)

Arguments

TreeMetacl	FlowSOM tree with meta-clusters, constructed by buildFSOMTree
markers	vector of markers for which PDF files of MFI will be generated
Title	title
rmClNb	number of smallest clusters to remove
treatmentTable	data frame containing a column 'files', a column 'Treatment' (case sensitive) and a column "NormaizationFactor"
globalScale	TRUE if color scale for markers is the same for each treatments

Examples

plotTreeSet(TreeMetaCl=CytoTree,markers=c("PD-1","CTLA-4"),Title="Experiment1",rmClNb=0,treatmentTable="Experiment1Table.csv",globalScale=TRUE)

gautierstoll/CytoSOM documentation built on May 16, 2020, 10:36 a.m.