plotViolin: Visualization violin plot of CYT

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

Description

Visualization violin plot of CYT

Usage

plotViolin(
  object,
  marker,
  color.by = "cluster.id",
  order.by = NULL,
  size = 1,
  text.angle = 0,
  main = "Violin plot CYT",
  plot.theme = theme_bw()
)

Arguments

object	A CYT object
marker	character. Markers used to plot
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).
order.by	vector. Order of color theme.
size	numeric. Size of the dot
text.angle	numberic. Text angle of the violin plot
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)

plotViolin(cyt, marker = "CD34")
plotViolin(cyt, marker = "CD34", order.by = "pseudotime")

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