plotTree: plot MST of FSPY

Description Usage Arguments Value Examples

View source: R/plotTree.R

Description

plot MST of FSPY

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

an FSPY 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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if (FALSE) {

plotTree(fspy)

plotTree(fspy, show.node.name = T)

plotTree(fspy, color.by = "CD43", show.node.name = T, cex.size = 1) +
    scale_colour_gradientn(colors = c("#00599F", "#EEEEEE", "#FF3222"))

plotTree(fspy, color.by = "D0.percent", show.node.name = T, cex.size = 1) +
    scale_colour_gradientn(colors = c("#00599F", "#EEEEEE", "#FF3222"))

plotTree(fspy, color.by = "D2.percent", show.node.name = T, cex.size = 1) +
    scale_colour_gradientn(colors = c("#00599F", "#EEEEEE", "#FF3222"))

plotTree(fspy, color.by = "pseudotime", cex.size = 1) +
    scale_colour_gradientn(colors = c("#F4D31D", "#FF3222","#7A06A0"))

}

JhuangLab/flowSpy documentation built on July 15, 2020, 8:31 a.m.