plot3D: Visualization of 3D data of CYT

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

Description

Visualization of 3D data of CYT

Usage

plot3D(
  object,
  item.use = c("PC1", "PC2", "PC3"),
  color.by = "stage",
  order.by = NULL,
  size = 1,
  angle = 60,
  scale.y = 0.8,
  category = "categorical",
  main = "3D plot of CYT",
  color.theme = NULL,
  ...
)

Arguments

object	A CYT object
item.use	character. Items use to 3D plot, axes x and y and z must be numeric.
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	character. Order of color theme.
size	numeric. size of the dot
angle	numberic. angle of the plot
scale.y	numeric. scale of y axis related to x- and z axis
category	character. numeric or categorical
main	character. title of the plot
color.theme	vector. Color themes use in the plot.
...	options to pass on to the scatterplot3d function.

Value

gplots figure

Examples

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

plot3D(cyt, item.use = c("DC_2","DC_1","DC_3"), color.by = "stage",
       size = 0.5, angle = 60, color.theme = c("#FF99FF","#7A06A0","#FF3222"))

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