PlotDimRed {FlowSOM} | R Documentation

## PlotDimRed

### Description

Plot a dimensionality reduction

### Usage

    PlotDimRed(
      fsom,
      colsToUse = fsom$map$colsUsed,
      colorBy = "metaclusters",
      cTotal = NULL,
      dimred = Rtsne::Rtsne,
      extractLayout = function(dimred) {     dimred$Y },
      label = TRUE,
      returnLayout = FALSE,
      seed = NULL,
      title = NULL,
      ...
    )

### Arguments

`fsom` | FlowSOM object, as generated by `BuildMST`
`colsToUse` | The columns used for the dimensionality reduction. Default = fsom$map$colsUsed.
`colorBy` | Defines how the dimensionality reduction will be colored. Can be "metaclusters" (default), "clusters" or a marker/channel/index.
`cTotal` | The total amount of cells to be used in the dimensionality reduction. Default is all the cells.
`dimred` | A dimensionality reduction function. Default = Rtsne::Rtsne. Alternatively, a data.frame or matrix with either equal number of rows to the fsom or an OriginalID column. Recommended to put cTotal to NULL when providing a matrix (or ensuring that the dimred corresponds to subsampling the flowSOM data for cTotal cells with the same seed).
`extractLayout` | A function to extract the coordinates from the results of the dimred default = function(dimred)dimred$Y.
`label` | If label = TRUE (default), labels are added to plot.
`returnLayout` | If TRUE, this function returns a dataframe with the layout of dimred and the original IDs and the plot. Default = FALSE.
`seed` | A seed for reproducibility.
`title` | A title for the plot.
`...` | Additional arguments to pass to dimred.

### Details

Plot a dimensionality reduction of fsom$data

### Value

A dimensionality reduction plot made in ggplot2

### Examples

       file <- system.file("extdata", "68983.fcs", package="FlowSOM")
       flowSOM.res <- FlowSOM(file, compensate = TRUE, transform = TRUE,
                      scale = TRUE,
                      colsToUse = c(9, 12, 14:18), nClus = 10, silent = FALSE,
                      xdim = 7, ydim = 7)
       PlotDimRed(flowSOM.res, cTotal = 5000, seed = 1, title = "t-SNE")
       PlotDimRed(flowSOM.res, cTotal = 5000, colorBy = "CD3", seed = 1,
                  title = "t-SNE")

[Package FlowSOM version 2.2.0 Index]