runPseudotime {flowSpy} | 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 = 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"))
    }

[Package flowSpy version 1.4.0 Index]