Description Usage Arguments Value Examples
Visualization of cluster data of CYT
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | plotCluster(
object,
item.use = c("PC_1", "PC_2"),
color.by = "cluster",
size.by = "cell.number.percent",
order.by = NULL,
size = 1,
alpha = 1,
category = "categorical",
show.cluser.id = FALSE,
show.cluser.id.size = 4,
main = "2D plot of cluster in 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). |
size.by |
character. Size of the dot |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | cyt.file <- system.file("extdata/cyt.rds", package = "CytoTree")
cyt <- readRDS(file = cyt.file)
plotCluster(cyt)
plotCluster(cyt, item.use = c("PC_1", "PC_2"))
plotCluster(cyt, item.use = c("PC_2", "PC_3"))
plotCluster(cyt, item.use = c("PC_2", "PC_3"), color.by = "CD43", category = "numeric")
plotCluster(cyt, item.use = c("PC_2", "PC_3"), color.by = "CD43", category = "numeric")
plotCluster(cyt, item.use = c("tSNE_1", "tSNE_2"))
plotCluster(cyt, item.use = c("tSNE_1", "tSNE_2"), show.cluser.id = TRUE)
plotCluster(cyt, item.use = c("DC_1", "DC_2"))
plotCluster(cyt, item.use = c("UMAP_1", "UMAP_2"))
|
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