@@ -13,8 +13,8 @@ Description: A simple framework to facilitate the comparison of pipelines involv

 	Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function 

 	then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations 

 	on the fly to avoid storing potentially large intermediate data.

-Imports: BiocParallel, S4Vectors, ComplexHeatmap, SingleCellExperiment, SummarizedExperiment, Seurat, data.table, 

-	matrixStats, Matrix, cluster, aricode, methods, utils, dplyr, grid, scales, scran, viridisLite, clue, randomcoloR, 

+Imports: BiocParallel, S4Vectors, ComplexHeatmap, SingleCellExperiment, SummarizedExperiment, Seurat, matrixStats, 

+	Matrix, cluster, aricode, methods, utils, dplyr, grid, scales, scran, viridisLite, clue, randomcoloR, 

 	ggplot2, cowplot, intrinsicDimension, scater, knitr, reshape2, stats, Rtsne, uwot, circlize, RColorBrewer

 Suggests: BiocStyle

 License: GPL

@@ -61,8 +61,6 @@ importFrom(circlize,colorRamp2)

 importFrom(clue,solve_LSAP)

 importFrom(cluster,silhouette)

 importFrom(cowplot,plot_grid)

-importFrom(data.table,data.table)

-importFrom(data.table,setorder)

 importFrom(dplyr,bind_cols)

 importFrom(dplyr,bind_rows)

 importFrom(grid,gpar)

@@ -104,13 +104,12 @@ parsePipNames <- function(x, setRowNames=FALSE, addcolumns=NULL){

 #' @return a matrix or data.frame

 #' @export

 #'

-#' @importFrom data.table data.table setorder

 #' @examples

 #' buildCombMatrix(list(param1=LETTERS[1:3], param2=1:2))

 buildCombMatrix <- function(alt, returnIndexMatrix=FALSE){

-  eg <- data.table(expand.grid(lapply(alt, FUN=seq_along)))

-  eg <- setorder(eg)

-  if(returnIndexMatrix) return(as.matrix(eg))

+  eg <- as.matrix(expand.grid(lapply(rev(alt), FUN=seq_along)))

+  eg <- eg[,seq(ncol(eg),1)]

+  if(returnIndexMatrix) return(eg)

   eg <- as.data.frame(eg)

   for(f in names(alt)){

     eg[,f] <- factor(alt[[f]][eg[,f]], levels=alt[[f]])

@@ -118,7 +117,6 @@ buildCombMatrix <- function(alt, returnIndexMatrix=FALSE){

   eg

 }

-#' @importFrom data.table data.table setorder

 .checkCombMatrix <- function(eg, alt){

   if(is.null(dim(eg))) 

     stop("`eg` should be a matrix or data.frame of indices or factors")

@@ -136,11 +134,15 @@ buildCombMatrix <- function(alt, returnIndexMatrix=FALSE){

       }

     }

   }

-  eg <- as.matrix(as.data.frame(setorder(data.table(eg))))

   if(any(is.na(eg))) stop("Final `eg` contains missing values!")

-  eg

+  .sortcols(eg)

 }

+.sortcols <- function(x){

+  xi <- x[,ncol(x)]

+  for(i in seq(ncol(x)-1,1)) xi <- xi+max(xi)*x[,i]

+  x[order(xi),]

+}

 #' getQualitativePalette

 #'

@@ -231,3 +233,4 @@ farthestPoint <- function(y, x=NULL){

               })

   order(d,decreasing=TRUE)[1]

 }

+