Plot2DScatters: Plot2DScatters

View source: R/5_plotFunctions.R

Plot2DScattersR Documentation

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")))


saeyslab/FlowSOM documentation built on July 6, 2024, 10:59 a.m.