@@ -80,6 +80,7 @@ import(Rcpp)

 import(RcppEigen)

 import(ggplot2)

 import(graphics)

+import(grid)

 import(gridExtra, except = c(combine))

 import(stats)

 importFrom(MAST,FromMatrix)

@@ -103,8 +104,7 @@ importFrom(grDevices,colorRampPalette)

 importFrom(grDevices,colors)

 importFrom(grDevices,hsv)

 importFrom(grDevices,rgb2hsv)

-importFrom(grid,grid.draw)

-importFrom(grid,grid.newpage)

+importFrom(grid,grid.pretty)

 importFrom(grid,unit)

 importFrom(gridExtra,grid.arrange)

 importFrom(gtable,gtable)

@@ -118,6 +118,7 @@ importFrom(methods,new)

 importFrom(plyr,mapvalues)

 importFrom(reshape2,melt)

 importFrom(scales,dscale)

+importFrom(scales,hue_pal)

 importFrom(stringi,stri_list2matrix)

 importFrom(umap,umap)

 importFrom(umap,umap.defaults)

@@ -74,8 +74,7 @@

 #'     z = clusters(celdaCGMod)$z, y = clusters(celdaCGMod)$y)

 #' @return list A list containing dendrogram information and the heatmap grob

 #' @import graphics

-#' @importFrom grid grid.newpage

-#' @importFrom grid grid.draw

+#' @import grid

 #' @export

 plotHeatmap <- function(counts,

     z = NULL,

@@ -78,6 +78,10 @@ differentialExpression <- function(counts,

         ngeneson = rep("", (length(cells1) + length(cells2))),

         stringsAsFactors = FALSE)

+    # explicitly load library SummarizedExperiment due to MAST package

+    # dependency error

+    library(SummarizedExperiment)

+    

     sca <- suppressMessages(MAST::FromMatrix(log_normalized_mat, cdat))

     cdr2 <- colSums(SummarizedExperiment::assay(sca) > 0)

     SummarizedExperiment::colData(sca)$cngeneson <- scale(cdr2)

@@ -552,7 +552,7 @@

                 width = 2 * textHeight,

                 gp = gpar(col = borderColor, fill = NA))

-            txt <- rev(range(grid.pretty(range(annotation[[i]],

+            txt <- rev(range(grid::grid.pretty(range(annotation[[i]],

                 na.rm = TRUE))))

             yy <- y - c(1, 7) * textHeight

@@ -966,6 +966,7 @@ vplayout <- function(x, y) {

 }

 ## changed the original clusterMat() in the pheatmap.r

+#' @importFrom scales hue_pal

 .clusterMat <- function(mat, labels, distance, method) {

     # this funciton is going to change the .clusterMat() in pheatmap

@@ -1237,7 +1238,8 @@ vplayout <- function(x, y) {

             }

         }

-        factorColors <- scales::dscale(factor(seq(1, count)), hue_pal(l = 75))

+        factorColors <- scales::dscale(factor(seq(1, count)),

+            scales::hue_pal(l = 75))

         contCounter <- 2

         for (i in seq(length(annotation))) {

@@ -1497,6 +1499,7 @@ vplayout <- function(x, y) {

 #' }

 #'

 #' pheatmap(test, clusteringCallback = callback)

+#' @importFrom grid grid.pretty

 #' @importFrom RColorBrewer brewer.pal

 semiPheatmap <- function(mat,

     color = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100),

@@ -1692,7 +1695,7 @@ semiPheatmap <- function(mat,

         breaks <- .generateBreaks(as.vector(mat), length(color))

     }

     if (legend & .is.na2(legendBreaks)) {

-        legend <- grid.pretty(range(as.vector(breaks)))

+        legend <- grid::grid.pretty(range(as.vector(breaks)))

         names(legend) <- legend

     }

     else if (legend & !.is.na2(legendBreaks)) {