runPseudotime {CytoTree}R Documentation

Calculation of Pseudotime

Description

calculation of Pseudotime based on KNN

Usage

runPseudotime(
  object,
  mode = "undirected",
  dim.type = c("raw", "pca", "tsne", "dc", "umap"),
  dim.use = seq_len(2),
  verbose = FALSE,
  ...
)

Arguments

object

An CYT object

mode

character. Specifies how igraph should interpret the supplied matrix. Possible values are: directed, undirected, upper, lower, max, min, plus.

dim.type

character. Type of dimensionality reduction method used to calculate pseudotime: raw, umap, tsne, dc and pca. By default is raw.

dim.use

numeric. Dimensions used to calculate pseudotime

verbose

logical. Whether to print calculation progress.

...

Parameters passing to calculation function.

Value

An CYT object

Examples


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

cyt <- runPseudotime(cyt, verbose = TRUE, dim.type = "raw")
cyt <- runPseudotime(cyt, verbose = TRUE, dim.type = "umap", dim.use = seq_len(2))
cyt <- runPseudotime(cyt, verbose = TRUE, dim.type = "tsne", dim.use = seq_len(2))
cyt <- runPseudotime(cyt, verbose = TRUE, dim.type = "dc", dim.use = seq_len(3))
cyt <- runPseudotime(cyt, verbose = TRUE, dim.type = "pca", dim.use = seq_len(3))

# tSNE plot colored by pseudotime
plot2D(cyt, item.use = c("tSNE_1", "tSNE_2"), category = "numeric",
       size = 1, color.by = "pseudotime") 
# UMAP plot colored by pseudotime
plot2D(cyt, item.use = c("UMAP_1", "UMAP_2"), category = "numeric",
       size = 1, color.by = "pseudotime") 



[Package CytoTree version 1.2.0 Index]