plotPseudotimeTraj: plotPseudotimeTraj

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

Description

plotPseudotimeTraj

Usage

plotPseudotimeTraj(
  object,
  cutoff = -1,
  markers = NULL,
  size = 0.5,
  alpha = 0.6,
  print.curve = TRUE,
  var.cols = FALSE,
  plot.theme = theme_bw()
)

Arguments

object	A CYT object
cutoff	numeric. Cutoff of trajectory value
markers	character. Markers used in the calculation progress
size	numeric. Size of the dot
alpha	numeric. Transparency (0-1) of the dot, default is 1.
print.curve	logical. Whether to perform curve fitting
var.cols	logical. Whether to plot stage
plot.theme	themes from ggplot2

Value

ggplot2 figure

Examples

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

plotPseudotimeTraj(cyt)
plotPseudotimeTraj(cyt, print.curve = FALSE)
plotPseudotimeTraj(cyt, var.cols = TRUE)

plotPseudotimeTraj(cyt, markers = c("CD43", "CD34"))

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