plotPseudotimeTraj: plotPseudotimeTraj

Description Usage Arguments Value Examples

View source: R/plotFSPY.R

Description

plotPseudotimeTraj

Usage

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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

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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.