plotPseudotimeTraj: plotPseudotimeTraj

In JhuangLab/flowSpy: 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	An FSPY 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

if (FALSE) {

plotPseudotimeTraj(fspy)
plotPseudotimeTraj(fspy, print.curve = F)
plotPseudotimeTraj(fspy, var.cols = T)

plotPseudotimeTraj(fspy) +
   scale_colour_gradientn(colors = c("#F4D31D", "#FF3222","#7A06A0"))

plotPseudotimeTraj(fspy, markers = c("CD43", "CD34")) +
scale_colour_gradientn(colors = c("#F4D31D", "#FF3222","#7A06A0"))

}

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