| plot2D {CytoTree} | R Documentation |
Visualization of 2D data of CYT
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()
)
object |
An 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 figure
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")