plotTree: plot MST of CYT

Description Usage Arguments Value Examples

View source: R/plotTree.R

Description

plot MST of CYT

Usage

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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

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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.