runPseudotime {flowSpy} | R Documentation |
calculation of Pseudotime based on KNN
runPseudotime( object, mode = "undirected", dim.type = c("raw", "pca", "tsne", "dc", "umap"), dim.use = 1:2, verbose = FALSE, ... )
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. |
An FSPY object
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")) }