R/Plot2DScatterPlot.R

In gautierstoll/CytoSOM: Easy use of FlowSOM

#' Plot2DScatterPlot
#'
#' Plot2DScatterPlot displays a 2D scatter plot of specified markers using the hexbin package.
#' @param TreeMetaCl object generated by buildFSOMTree function
#' @param Title title of the 2D scatter plot
#' @param Marker1 marker to plot on the abscissa ("x")
#' @param Marker2 marker to plot on the ordinate ("y")
#' @param minct minimun count of cells to display as a polygon on the plot
#' @param style appareance of the polygons for the plot, that can be "colorscape","nestle.lattice", "nestle.centroids"...
#' @return PDF file of the chosen 2D scatter plot, that is saved in the working directory
#' @examples Plot2DScatterPlot(CytoTree,"Experiment 1","FSC-A","SSC-A",100,"colorscale")
#' @export


Plot2DScatterPlot<-function(TreeMetaCl,Title,Marker1,Marker2,mincnt,style){
  library(hexbin)
  ClustersData<-as.data.frame(TreeMetaCl$fSOMTree$map$mapping)
  MarkersData<-as.data.frame(TreeMetaCl$fSOMTree$data)
  PrettyNames<-as.data.frame(TreeMetaCl$fSOMTree$prettyColnames)
  PrettyNames$UglyNames<-row.names(PrettyNames)
  names(PrettyNames)[1]<-"PrettyNames"
  colnames(MarkersData)<-PrettyNames$PrettyNames[match(colnames(MarkersData),PrettyNames$UglyNames)]
  FrameMarkers<-cbind(ClustersData,MarkersData)
  names(FrameMarkers)[1]<-"Clusters"
  MetaclFrame<-as.data.frame(TreeMetaCl$metaClNumber)
  MetaclFrame$Clusters<-c(1:nrow(MetaclFrame))
  names(MetaclFrame)[1]<-"Metaclusters"
  FrameMarkers$Metaclusters<-MetaclFrame[match(x=FrameMarkers$Clusters, table = MetaclFrame$Clusters),"Metaclusters"]

  x=FrameMarkers[[Marker1]]
  y=FrameMarkers[[Marker2]]
  bin=hexbin(x,y)
  pdf(file=NoSpCharForFile(paste(Title)),"2D_Scatterplot.jpeg")
  gplot.hexbin(bin,style,xlab = Marker1 ,ylab = Marker2 ,legend = 0.7,lcex = 0.5,mincnt,
               clip = "on",minarea = 0.005,maxarea = 1)
  dev.off()
}