plotTree: plot MST of CYT

In JhuangLab/CytoTree: A Toolkit for Flow And Mass Cytometry Data

Description

plot MST of CYT

Usage

plotTree(
  object,
  cex.size = 1,
  color.by = "cell.number",
  size.by = "cell.number",
  as.tree = FALSE,
  root.id = NULL,
  show.node.name = FALSE
)

Arguments

object	a CYT object
cex.size	numeric. size cex of the dot
color.by	numeric. size color theme of the dot
size.by	numeric. size theme of the dot
as.tree	logical. Whether to show node as tree
root.id	numeric. Root id of the tree, if as.tree is TRUE
show.node.name	logical. whether to show node name

Value

ggplot2 figure

Examples

cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree")
cyt <- readRDS(file = cyt.file)

plotTree(cyt)

plotTree(cyt, show.node.name = TRUE)

plotTree(cyt, color.by = "CD43", show.node.name = TRUE, cex.size = 1) 

plotTree(cyt, color.by = "D0.percent", show.node.name = TRUE, cex.size = 1) 

plotTree(cyt, color.by = "D2.percent", show.node.name = TRUE, cex.size = 1) 

plotTree(cyt, color.by = "pseudotime", cex.size = 1)

JhuangLab/CytoTree documentation built on Nov. 16, 2020, 7:23 a.m.