plotCluster {CytoTree} | R Documentation

## Visualization of cluster data of CYT

### Description

Visualization of cluster data of CYT

### Usage

    plotCluster(
      object,
      item.use = c("PC_1", "PC_2"),
      color.by = "cluster",
      size.by = "cell.number.percent",
      order.by = NULL,
      size = 1,
      alpha = 1,
      category = "categorical",
      show.cluser.id = FALSE,
      show.cluser.id.size = 4,
      main = "2D plot of cluster in CYT",
      plot.theme = theme_bw()
    )

### Arguments

`object` | An CYT object
`item.use` | character. Items use to 2D plot, axes x and y must be numeric.
`color.by` | character. Dot or mesh color by which character. It can be one of the column of plot.meta, or it can be just "density" (the default value).
`size.by` | character. Size of the dot
`order.by` | vector. Order of color theme.
`size` | numeric. Size of the dot
`alpha` | numberic. Transparency (0-1) of the dot, default is 1.
`category` | character. numeric or categorical
`show.cluser.id` | logical. Whether to show cluster id in the plot.
`show.cluser.id.size` | numeric. Size of the cluster id.
`main` | character. Title of the plot.
`plot.theme` | themes from `ggplot2`

### Value

ggplot2 figure

### Examples

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

    plotCluster(cyt)

    plotCluster(cyt, item.use = c("PC_1", "PC_2"))
    plotCluster(cyt, item.use = c("PC_2", "PC_3"))
    plotCluster(cyt, item.use = c("PC_2", "PC_3"), color.by = "CD43", category = "numeric")
    plotCluster(cyt, item.use = c("PC_2", "PC_3"), color.by = "CD43", category = "numeric")

    plotCluster(cyt, item.use = c("tSNE_1", "tSNE_2"))
    plotCluster(cyt, item.use = c("tSNE_1", "tSNE_2"), show.cluser.id = TRUE)

    plotCluster(cyt, item.use = c("DC_1", "DC_2"))

    plotCluster(cyt, item.use = c("UMAP_1", "UMAP_2"))

[Package CytoTree version 1.0.3 Index]