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 |
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 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")