Plot1DScatters: Plot1DScatters

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

Plot1DScatters

Description

Function to draw 1D scatter plots of FlowSOM (meta)clusters

Usage

Plot1DScatters(
  fsom,
  channels = fsom$map$colsUsed,
  clusters = NULL,
  metaclusters = NULL,
  maxBgPoints = 3000,
  sizeBgPoints = 0.5,
  colBgPoints = "gray",
  maxPoints = 1000,
  sizePoints = 0.5,
  yLim = NULL,
  xLabels = c("marker"),
  centers = FALSE,
  colors = NULL,
  ncol = NULL,
  nrow = NULL,
  width = NULL,
  height = NULL,
  plotFile = "1DScatterPlots.png"
)

Arguments

fsom	FlowSOM object, as created by FlowSOM
channels	Vector in which each element is a channel or a marker
clusters	Vector with indices of clusters of interest
metaclusters	Vector with indices of metaclusters of interest
maxBgPoints	Maximum number of background cells to plot
sizeBgPoints	Size of the background cells
colBgPoints	Color of background cells
maxPoints	Maximum number of (meta)cluster cells to plot
sizePoints	Size of the (meta)cluster cells
yLim	Optional vector of a lower and upper limit of the y-axis
xLabels	Determines the label of the x-axis. Can be "marker" and\or "channel" or abbreviations. Default = "marker".
centers	Add cluster centers to plot. Default = FALSE.
colors	Vector of colors for all the cells in the selected nodes. First the clusters are colored, then the metaclusters. If NULL, the default ggplot colors, are used.
ncol	Number of columns in the final plot, optional
nrow	Number of rows in the final plot, optional
width	Width of png file. By default NULL the width parameter is estimated based on the input.
height	Height of png file. By default NULL the width parameter is estimated based on the input.
plotFile	If a filepath for a png is given (default = 1DScatterPlots.png), the plots will be plotted in the corresponding png file. If NULL, a list of ggplot objects will be returned

Details

Plot multiple 1D 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 1D scatter plots of the clusters and metaclusters of interest
Plot1DScatters(fsom = flowSOM.res,
              channels = c("PE-Cy7-A", "PE-Cy5-A"),
              clusters = c(1, 48, 49, 82, 95),
              metaclusters = list(c(1, 4), 9),
              xLabels = c("marker", "channel"))
Plot1DScatters(flowSOM.res, 
              metaclusters = 4, 
              clusters = c(1, 2),
              colors = c("red", "green", "blue"))                       

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