circ.tree: Circular dendrogram tree

In jgarces02/FlowCT: A semi-automated workflow for deconvolution of immunophenotypic data and objective reporting on large datasets

Circular dendrogram tree

Description

This function plots a circular dendrogram and a heatmap according a fcs.SCE. Every leaf has a different colored point size regarding the cell type and the frequency for each cluster. For additional information go to ggtree package.

Usage

circ.tree(
  fcs.SCE,
  assay.i = "normalized",
  cell.clusters,
  dist.method = "euclidean",
  hclust.method = "average",
  nodes = "display",
  open.angle = 100,
  scale.size = 10,
  colors, 
  labels = c(T, 0.2)
)

Arguments

fcs.SCE	A fcs.SCE object generated through FlowCT::fcs.SCE().
assay.i	Name of matrix stored in the fcs.SCE object from which drawing the circular tree. Default = "normalized".
cell.clusters	Name of column containing clusters identified through FlowCT::clustering.flow().
dist.method	Distance method measurement to be used. Possible values are "euclidean" (default), "maximum", "manhattan", "canberra", "binary" or "minkowski".
hclust.method	Hierarchical clustering method to be used. Possible values are "average" (default), "ward.D", "ward.D2", "single", "complete", "mcquitty", "median" or "centroid".
nodes	If "display" (default), nodes will be numered. If contains a numeric vector with node numbers, areas defined from these nodes will be differently colored.
open.angle	Angle aperture circular layout. Default = 100.
scale.size	Numerical value indicating how much scale points in the dendogram terminal nodes. Default = 10.
colors	Vector with colors for plotting.
labels	Two values indicating if labels should be displayed (default, TRUE) and the offset value (for separating labels from tree tips, 0.2 as default).

Examples

## Not run: 
# step 1: display all node numbers to select how to coloring areas
circ.tree(fcs.SCE = fcsL, cell.clusters = "SOM_L_named", nodes = "display")

# step 2: color areas indicating node numbers
circ.tree(fcs.SCE = fcsL, cell.clusters = "SOM_L_named", nodes = c(17, 25))

## End(Not run)

jgarces02/FlowCT documentation built on March 28, 2023, 12:42 p.m.