Description Usage Arguments Value Examples
calculation of Pseudotime based on KNN
1 2 3 4 5 6 7 8 |
object |
A 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. |
A CYT object
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | 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")
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