R/RCA-class.R

In linquynus/RCAv2-beta: Reference Component Analysis

#' RCA Class
#'
#' @export
#'
RCAConstruct <- setRefClass(Class = "RCA", 
			    fields = list(raw.data = "Matrix", 
					  data = "Matrix", 
					  projection.data = "Matrix", 
					  clustering.out = "list",
					  umap.coordinates = "data.frame",
					  cell.Type.Estimate = "list",
					  baseColors = "list",
					  rRank = "list",
					  cScore = "list",
					  DE.genes = "list"))

RCAConstruct$methods(show=function(){
		     print("RCA reference class object")
			     dataSize=dim(raw.data);
			     print(paste0("Raw data: ",dataSize[2]," cells and ",dataSize[1]," features."))

			     dataSize=dim(data);
			     print(paste0("Normalized data: ",dataSize[2]," cells and ",dataSize[1]," features."))

			     dataSize=dim(projection.data);
			     print(paste0("Projection data: ",dataSize[2]," cells to ",dataSize[1]," cell-types."))

			     nDim=dim(umap.coordinates)[2]
			     print(paste0("UMAP coordinates are available for ",nDim," dimensions."))

			     dataSize=length(unique(clustering.out$dynamicColorsList[[1]]));
			     print(paste0("The data set contains ",dataSize," RCA clusters."))

			     dataSize=length(unique(cell.Type.Estimate));
			     print(paste0("The data set contains ",dataSize," unique cell types."))


		})