PlotDimRed: PlotDimRed

In SofieVG/FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

PlotDimRed

Description

Plot a dimensionality reduction

Usage

PlotDimRed(
  fsom,
  colsToUse = fsom$map$colsUsed,
  colorBy = "metaclusters",
  colors = NULL,
  lim = NULL,
  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 abbreviations) or a marker/channel/index.
colors	A vector of custom colors. Default returns ggplot colors for categorical variables and the FlowSOM colors for continuous variables. When using a categorical variable, the vector must be as long as the levels of the categorical variable.
lim	Limits for the colorscale
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")
   

SofieVG/FlowSOM documentation built on Feb. 1, 2024, 11:33 a.m.