plot2D: Visualization of 2D data of CYT

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

Description

Visualization of 2D data of CYT

Usage

plot2D(
  object,
  item.use = c("PC_1", "PC_2"),
  color.by = "stage",
  order.by = NULL,
  size = 1,
  alpha = 1,
  category = "categorical",
  show.cluser.id = FALSE,
  show.cluser.id.size = 4,
  main = "2D plot of CYT",
  plot.theme = theme_bw()
)

Arguments

object	A CYT object
item.use	character. Items use to 2D plot, axes x and y 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	vector. Order of color theme.
size	numeric. Size of the dot
alpha	numberic. Transparency (0-1) of the dot, default is 1.
category	character. numeric or categorical
show.cluser.id	logical. Whether to show cluster id in the plot.
show.cluser.id.size	numeric. Size of the cluster id.
main	character. Title of the plot.
plot.theme	themes from ggplot2

Value

ggplot2 figure

Examples

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

# Default plot
plot2D(cyt)

# PCA plot
plot2D(cyt, item.use = c("PC_1", "PC_2"))
plot2D(cyt, item.use = c("PC_1", "PC_2"), color.by = "cluster.id")
plot2D(cyt, item.use = c("PC_1", "PC_2"), color.by = "stage")
plot2D(cyt, item.use = c("PC_2", "PC_3"), color.by = "stage") 
plot2D(cyt, item.use = c("PC_2", "PC_3"), color.by = "CD43",
       category = "numeric")
plot2D(cyt, item.use = c("PC_2", "PC_3"), color.by = "CD43",
       category = "numeric")

# tSNE plot
plot2D(cyt, item.use = c("tSNE_1", "tSNE_2"))
plot2D(cyt, item.use = c("tSNE_1", "tSNE_2"), color.by = "stage")
plot2D(cyt, item.use = c("tSNE_1", "tSNE_2"), color.by = "cluster.id",
       alpha = 0.5, main = "tSNE Plot")
plot2D(cyt, item.use = c("tSNE_1", "tSNE_2"), color.by = "cluster.id",
       alpha = 1, main = "tSNE Plot", show.cluser.id = TRUE)
plot2D(cyt, item.use = c("tSNE_1", "tSNE_2"), color.by = "CD43",
       category = "numeric", size = 3)
plot2D(cyt, item.use = c("tSNE_1", "tSNE_2"), color.by = "stage")

# Diffusion Map plot
plot2D(cyt, item.use = c("DC_1", "DC_2"))
plot2D(cyt, item.use = c("DC_1", "DC_2"), color.by = "stage")
plot2D(cyt, item.use = c("DC_2", "DC_3"), color.by = "cluster.id",
       alpha = 0.5, main = "Diffusion Map Plot")
plot2D(cyt, item.use = c("DC_2", "DC_3"), color.by = "cluster.id",
       alpha = 1, main = "Diffusion Map Plot", show.cluser.id = TRUE)
plot2D(cyt, item.use = c("DC_1", "DC_2"), color.by = "CD43",
       category = "numeric", size = 3)

# UMAP plot
plot2D(cyt, item.use = c("UMAP_1", "UMAP_2"))
plot2D(cyt, item.use = c("UMAP_1", "UMAP_2"), color.by = "stage")
plot2D(cyt, item.use = c("UMAP_1", "UMAP_2"), color.by = "cluster.id",
       alpha = 0.5, main = "UMAP Plot")
plot2D(cyt, item.use = c("UMAP_1", "UMAP_2"), color.by = "cluster.id",
       alpha = 1, main = "UMAP Plot", show.cluser.id = TRUE)
plot2D(cyt, item.use = c("UMAP_1", "UMAP_2"), color.by = "CD43",
       category = "numeric", size = 3)
plot2D(cyt, item.use = c("UMAP_1", "UMAP_2"), color.by = "stage")

# Marker Plot
plot2D(cyt, item.use = c("CD43", "CD90"), color.by = "cluster.id")
plot2D(cyt, item.use = c("CD34", "CD90"), color.by = "CD43",
       category = "numeric", size = 3)

# Pseudotime
plot2D(cyt, item.use = c("pseudotime", "CD43"), color.by = "stage")

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