plotPseudotimeTraj {CytoTree}R Documentation

plotPseudotimeTraj

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

An 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"))




[Package CytoTree version 1.2.0 Index]