Plot2DScatters {FlowSOM} | R Documentation |
Function to draw 2D scatter plots of FlowSOM (meta)clusters
Plot2DScatters( fsom, channelpairs, clusters = NULL, metaclusters = NULL, maxBgPoints = 3000, sizeBgPoints = 0.5, maxPoints = 1000, sizePoints = 0.5, xLim = NULL, yLim = NULL, density = TRUE, centers = TRUE, color = NULL, plotFile = "2DScatterPlots.png" )
fsom |
FlowSOM object, as created by |
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 clusters of interest |
metaclusters |
Vector or list (to combine multiple metaclusters in one plot) with 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 |
A vector of a lower and upper limit of the x-axis |
yLim |
A vector of a lower and upper limit of the y-axis |
density |
Default is |
centers |
Default is |
color |
Colors for all the cells in the selected nodes
(ordered list). If |
plotFile |
If a filepath for a png is given (default =
2DScatterPlots.png), the plots will be plotted in
the corresponding png file. If |
Plot multiple 2D scatter plots in a png file. A subset of fsom$data is plotted in grey, and those of the selected clusters and metaclusters are plotted in color.
If plot
is TRUE
, nothing is returned and a plot is
drawn in which background cells are plotted in grey and the cells of
the selected nodes in color. If plot
is FALSE
, a ggplot
objects list is returned.
# 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, color = list(c("red", "green")))