runPseudotime: Calculation of Pseudotime

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

Description

calculation of Pseudotime based on KNN

Usage

runPseudotime(
  object,
  mode = "undirected",
  dim.type = c("raw", "pca", "tsne", "dc", "umap"),
  dim.use = 1:2,
  verbose = FALSE,
  ...
)

Arguments

object	An FSPY 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 FSPY object

Examples

if (FALSE) {

fspy <- runPseudotime(fspy, verbose = TRUE, dim.type = "raw")
fspy <- runPseudotime(fspy, verbose = TRUE, dim.type = "umap", dim.use = 1:2)
fspy <- runPseudotime(fspy, verbose = TRUE, dim.type = "tsne", dim.use = 1:2)
fspy <- runPseudotime(fspy, verbose = TRUE, dim.type = "dc", dim.use = 1:3)
fspy <- runPseudotime(fspy, verbose = TRUE, dim.type = "pca", dim.use = 1:3)

# tSNE plot colored by pseudotime
plot2D(fspy, item.use = c("tSNE_1", "tSNE_2"), category = "numeric",
       size = 1, color.by = "pseudotime") +
       scale_colour_gradientn(colors = c("#F4D31D", "#FF3222","#7A06A0"))
# UMAP plot colored by pseudotime
plot2D(fspy, item.use = c("UMAP_1", "UMAP_2"), category = "numeric",
       size = 1, color.by = "pseudotime") +
       scale_colour_gradientn(colors = c("#F4D31D", "#FF3222","#7A06A0"))
}

JhuangLab/flowSpy documentation built on July 15, 2020, 8:31 a.m.