Remove gdata dependency

DESCRIPTION

@@ -43,7 +43,6 @@ Imports:
     irlba,
     reshape2,
     gplots,
-    gdata,
     Rcpp (>= 0.11.0),
     tclust,
     ranger,
@@ -102,6 +101,7 @@ Collate:
     'zfRenderSeurat.R'
 RoxygenNote: 6.0.1
 Suggests:
+    gdata,
     testthat,
     loomR,
     phateR,

NAMESPACE

@@ -331,8 +331,6 @@ importFrom(dtw,dtw)
 importFrom(fitdistrplus,fitdist)
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)
-importFrom(gdata,drop.levels)
-importFrom(gdata,interleave)
 importFrom(ggplot2,annotation_raster)
 importFrom(ggridges,geom_density_ridges)
 importFrom(ggridges,theme_ridges)

R/interaction.R

@@ -921,8 +921,6 @@ StashIdent <- function(object, save.name = "oldIdent") {
 #'
 #' @return A Seurat object where object@@ident has been appropriately modified
 #'
-#' @importFrom gdata drop.levels
-#'
 #' @export
 #'
 #' @examples
@@ -954,7 +952,7 @@ SetIdent <- function(object, cells.use = NULL, ident.use = NULL) {
     )
   )
   object@ident[cells.use] <- ident.use
-  object@ident <- drop.levels(x = object@ident)
+  object@ident <- droplevels(x = object@ident)
   return(object)
 }
 
@@ -1194,7 +1192,7 @@ RenameCells <- function(object, add.cell.id = NULL, new.names = NULL,
   colnames(object@raw.data) <- new.rawdata.names
   rownames(object@meta.data) <- new.cell.names
   object@cell.names <- new.cell.names
-  
+
   if (for.merge) {
     return(object)
   }

R/zfRenderSeurat.R

@@ -538,9 +538,13 @@ zf.insitu.ventral <- function(seuratObject, gene, label=TRUE, ...) {
   view3d(zoom = .75, userMatrix = rotMat, fov = 0)
 }
 
+# @importFrom gdata interleave
+#' @importFrom utils installed.packages
 #' @export
-#' @importFrom gdata interleave
 zf.insitu.side <- function(expressionMatrix, nonmirror = TRUE, mirror = TRUE) {
+  if (!'gdata' %in% rownames(x = installed.packages())) {
+    stop("Please install gdata")
+  }
   # Determine geometry
   tierBins <- 30 # 1 bin per cell tier.
   DVBins <- 64 # 1 bin every 5.625 degrees; compatible with our current 8-bin system.
@@ -641,23 +645,23 @@ zf.insitu.side <- function(expressionMatrix, nonmirror = TRUE, mirror = TRUE) {
     }
   }
   # Take the coordinates and reformat the lists to pass to RGL
-  quadX <- interleave(
+  quadX <- gdata::interleave(
     drawEmbryo$x1,
     drawEmbryo$x2,
     drawEmbryo$x3,
     drawEmbryo$x4,
     drop = TRUE
   )
   dim(x = quadX) <- c(dim(x = quadX)[1] * dim(x = quadX)[2], 1)
-  quadY <- interleave(
+  quadY <- gdata::interleave(
     drawEmbryo$y1,
     drawEmbryo$y2,
     drawEmbryo$y3,
     drawEmbryo$y4,
     drop = TRUE
   )
   dim(x = quadY) <- c(dim(x = quadY)[1] * dim(x = quadY)[2], 1)
-  quadZ <- interleave(
+  quadZ <- gdata::interleave(
     drawEmbryo$z1,
     drawEmbryo$z2,
     drawEmbryo$z3,