plotCluster: Visualization of cluster data of CYT

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

Description

Visualization of cluster data of CYT

Usage

plotCluster(
  object,
  item.use = c("PC_1", "PC_2"),
  color.by = "cluster",
  size.by = "cell.number.percent",
  order.by = NULL,
  size = 1,
  alpha = 1,
  category = "categorical",
  show.cluser.id = FALSE,
  show.cluser.id.size = 4,
  main = "2D plot of cluster in CYT",
  plot.theme = theme_bw()
)

Arguments

object	An CYT object
item.use	character. Items use to 2D plot, axes x and y must be numeric.
color.by	character. Dot or mesh color by which character. It can be one of the column of plot.meta, or it can be just "density" (the default value).
size.by	character. Size of the dot
order.by	vector. Order of color theme.
size	numeric. Size of the dot
alpha	numberic. Transparency (0-1) of the dot, default is 1.
category	character. numeric or categorical
show.cluser.id	logical. Whether to show cluster id in the plot.
show.cluser.id.size	numeric. Size of the cluster id.
main	character. Title of the plot.
plot.theme	themes from ggplot2

Value

ggplot2 figure

Examples

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

plotCluster(cyt)

plotCluster(cyt, item.use = c("PC_1", "PC_2"))
plotCluster(cyt, item.use = c("PC_2", "PC_3"))
plotCluster(cyt, item.use = c("PC_2", "PC_3"), color.by = "CD43", category = "numeric")
plotCluster(cyt, item.use = c("PC_2", "PC_3"), color.by = "CD43", category = "numeric")

plotCluster(cyt, item.use = c("tSNE_1", "tSNE_2"))
plotCluster(cyt, item.use = c("tSNE_1", "tSNE_2"), show.cluser.id = TRUE)

plotCluster(cyt, item.use = c("DC_1", "DC_2"))

plotCluster(cyt, item.use = c("UMAP_1", "UMAP_2"))

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