Plot2DScatters: Plot2DScatters

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

Plot2DScatters

Description

Function to draw 2D scatter plots of FlowSOM (meta)clusters

Usage

Plot2DScatters(
  fsom,
  channelpairs,
  clusters = NULL,
  metaclusters = NULL,
  maxBgPoints = 3000,
  sizeBgPoints = 0.5,
  maxPoints = 1000,
  sizePoints = 0.5,
  xLim = NULL,
  yLim = NULL,
  xyLabels = c("marker"),
  density = TRUE,
  centers = TRUE,
  colors = NULL,
  plotFile = "2DScatterPlots.png"
)

Arguments

fsom	FlowSOM object, as created by FlowSOM
channelpairs	List in which each element is a pair of channel or marker names
clusters	Vector or list (to combine multiple clusters in one plot) with indices of clusters of interest
metaclusters	Vector or list (to combine multiple metaclusters in one plot) with indices of metaclusters of interest
maxBgPoints	Maximum number of background cells to plot
sizeBgPoints	Size of the background cells
maxPoints	Maximum number of (meta)cluster cells to plot
sizePoints	Size of the (meta)cluster cells
xLim	Optional vector of a lower and upper limit of the x-axis
yLim	Optional vector of a lower and upper limit of the y-axis
xyLabels	Determines the label of the x- and y-axis. Can be "marker" and\or "channel" or abbrevations. Default = "marker".
density	Default is TRUE to color the (meta)cluster points according to density. Set to FALSE to use a plain color
centers	Default is TRUE to show the cluster centers
colors	Colors for all the cells in the selected nodes (ordered list). First the clusters are colored, then the metaclusters. If NULL, the default ggplot colors, indexed by metacluster number, are used.
plotFile	If a filepath for a png is given (default = 2DScatterPlots.png), the plots will be plotted in the corresponding png file. If NULL, a list of ggplot objects will be returned

Details

Plot multiple 2D scatter plots in a png file. A subset of fsom$data is plotted in gray, and those of the selected clusters and metaclusters are plotted in color.

Value

If plot is TRUE, nothing is returned and a plot is drawn in which background cells are plotted in gray and the cells of the selected nodes in color. If plot is FALSE, a ggplot objects list is returned.

Examples

# Identify the files
fcs <- flowCore::read.FCS(system.file("extdata", "68983.fcs", 
                                      package = "FlowSOM"))

# Build a FlowSOM object
flowSOM.res <- FlowSOM(fcs, 
                       scale = TRUE,
                       compensate = TRUE, 
                       transform = TRUE,
                       toTransform = 8:18, 
                       colsToUse = c(9, 12, 14:18),
                       nClus = 10,
                       seed = 1)

# Make the 2D scatter plots of the clusters and metaclusters of interest
Plot2DScatters(fsom = flowSOM.res,
               channelpairs = list(c("PE-Cy7-A", "PE-Cy5-A"),
                                   c("PE-Texas Red-A", "Pacific Blue-A")),
               clusters = c(1, 48, 49, 82, 95),
               metaclusters = list(c(1, 4), 9),
               density = FALSE)
               
Plot2DScatters(fsom = flowSOM.res,
               channelpairs = list(c("PE-Texas Red-A", "Pacific Blue-A")),
               metaclusters = list(c(1, 4)),
               density = FALSE,
               colors = list(c("red", "green")))

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