@@ -78,8 +78,10 @@ exportMethods(runParams)

 exportMethods(sampleLabel)

 import(Rcpp)

 import(RcppEigen)

+import(data.table, except = melt)

 import(foreach)

 import(ggplot2)

+import(grDevices)

 import(graphics)

 import(grid)

 import(gridExtra, except = c(combine))

@@ -117,6 +119,7 @@ importFrom(methods,is)

 importFrom(methods,new)

 importFrom(plyr,mapvalues)

 importFrom(reshape2,melt)

+importFrom(scales,brewer_pal)

 importFrom(scales,dscale)

 importFrom(scales,hue_pal)

 importFrom(stringi,stri_list2matrix)

@@ -26,7 +26,7 @@

 #' clusterDiffexpRes = differentialExpression(celdaCGSim$counts,

 #'     celdaCGMod, c1 = c(1, 2))

 #' @export

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

+#' @rawNamespace import(data.table, except = melt)

 #' @importFrom MAST FromMatrix

 #' @importFrom MAST zlm

 #' @importFrom MAST summary

@@ -81,7 +81,7 @@ differentialExpression <- function(counts,

     # 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)

@@ -216,6 +216,7 @@ plotDimReduceFeature <- function(dim1,

 #'  This matrix should be the same as the one used to generate `celdaMod`.

 #' @param celdaMod Celda object of class "celda_G" or "celda_CG".

 #' @param modules Character vector. Module(s) from celda model to be plotted.

+#' e.g. c("1", "2").

 #' @param rescale Logical.

 #'  Whether rows of the matrix should be rescaled to [0, 1]. Default TRUE.

 #' @param size Numeric. Sets size of point on plot. Default 1.

@@ -237,7 +238,7 @@ plotDimReduceFeature <- function(dim1,

 #' plotDimReduceModule(

 #'     dim1 = celdaTsne[, 1], dim2 = celdaTsne[, 2],

 #'     counts = celdaCGSim$counts, celdaMod = celdaCGMod,

-#'     modules = c("L1", "L2"))

+#'     modules = c("1", "2"))

 #' @export

 plotDimReduceModule <-

     function(dim1,

@@ -252,6 +253,7 @@ plotDimReduceModule <-

         colorLow = "grey",

         colorMid = NULL,

         colorHigh = "blue") {

+

         factorized <- factorizeMatrix(celdaMod = celdaMod,

             counts = counts)

         matrix <- factorized$proportions$cell

@@ -585,6 +585,7 @@ vplayout <- function(x, y) {

 #' @importFrom gtable gtable_height

 #' @importFrom gtable gtable_width

 #' @importFrom gtable gtable_add_grob

+#' @import grDevices

 .heatmapMotor <- function(matrix,

         borderColor,

         cellWidth,

@@ -1218,6 +1219,7 @@ vplayout <- function(x, y) {

 }

 #' @importFrom scales dscale

+#' @importFrom scales brewer_pal

 .generateAnnotationColours <- function(annotation,

     annotationColors,

     drop) {

@@ -1265,7 +1267,7 @@ vplayout <- function(x, y) {

                     factorColors <- factorColors[-ind]

                 } else {

                     annotationColors[[names(annotation)[i]]] <-

-                        brewer_pal("seq", contCounter)(5)[seq(4)]

+                        scales::brewer_pal("seq", contCounter)(5)[seq(4)]

                     contCounter <- contCounter + 1

                 }

             }

@@ -23,7 +23,8 @@ This matrix should be the same as the one used to generate `celdaMod`.}

 \item{celdaMod}{Celda object of class "celda_G" or "celda_CG".}

-\item{modules}{Character vector. Module(s) from celda model to be plotted.}

+\item{modules}{Character vector. Module(s) from celda model to be plotted.

+e.g. c("1", "2").}

 \item{rescale}{Logical.

 Whether rows of the matrix should be rescaled to [0, 1]. Default TRUE.}

@@ -61,5 +62,5 @@ celdaTsne <- celdaTsne(counts = celdaCGSim$counts,

 plotDimReduceModule(

     dim1 = celdaTsne[, 1], dim2 = celdaTsne[, 2],

     counts = celdaCGSim$counts, celdaMod = celdaCGMod,

-    modules = c("L1", "L2"))

+    modules = c("1", "2"))

 }