@@ -14,8 +14,8 @@

 #' @param cellIndex A vector that can subset the input SCE object by columns

 #' (cells). Alternatively, it can be a vector identifying cells in another

 #' cell list indicated by \code{featureIndexBy}. Default \code{NULL}.

-#' @param scale Whether to perform z-score scaling on each row. Default

-#' \code{TRUE}.

+#' @param scale Whether to perform z-score or min-max scaling on each row.Choose from \code{"zscore"}, \code{"min-max"} or default

+#' \code{TRUE} or \code{FALSE}

 #' @param trim A 2-element numeric vector. Values outside of this range will be

 #' trimmed to their nearst bound. Default \code{c(-2, 2)}

 #' @param featureIndexBy A single character specifying a column name of

@@ -103,8 +103,11 @@

 #' @importFrom stringr str_replace_all str_c

 #' @importFrom stats prcomp quantile

 #' @importFrom dplyr select arrange group_by count ungroup mutate one_of desc

-#' @importFrom tidyr spread

+#' @importFrom tidyr spread unite column_to_rownames remove_rownames

 #' @importFrom grid gpar

+#' @importFrom ComplexHeatmap anno_barplot

+#' @importFrom rlang .data

+#' 

 plotSCEHeatmap <- function(inSCE, useAssay = 'logcounts', useReducedDim = NULL,

                            doLog = FALSE, featureIndex = NULL, cellIndex = NULL,

                            scale = TRUE, trim = c(-2,2),

@@ -238,14 +241,26 @@ plotSCEHeatmap <- function(inSCE, useAssay = 'logcounts', useReducedDim = NULL,

     }

     featureIndex <- which(featureIndex)

   }

-  colnames(SCE) <- colLabelName

-  rownames(SCE) <- rowLabelName

+  if(is.null(colLabelName)){

+    colnames(SCE) <- NULL

+  }

+  else{

+    colnames(SCE) <- colLabelName

+  }

+ 

+  if(is.null(rowLabelName)){

+    rownames(SCE) <- NULL

+  }

+  else{

+    rownames(SCE) <- rowLabelName

+  }

+  

   SCE <- SCE[featureIndex, cellIndex]

   ### Scaling should be done before aggregating

   if (isTRUE(doLog)) assay(SCE) <- log1p(assay(SCE))

   if(isTRUE(scale)) scale <- "zscore"

   if ((scale == "zscore")) {

-    assay(SCE) <- as.matrix(scale(assay(SCE)))

+    assay(SCE) <- as.matrix(base::scale(assay(SCE)))

   } else if (scale ==  "min_max") {

     assay(SCE) <- as.matrix(.minmax(assay(SCE)))

   }    

@@ -263,7 +278,14 @@ plotSCEHeatmap <- function(inSCE, useAssay = 'logcounts', useReducedDim = NULL,

     # TODO: `aggregateAcrossCells` produce duplicated variables in colData

     # and unwanted "ncell" variable even if I set `store.number = NULL`.

    #colData(SCE) <- colData(SCE)[,c(aggregateCol),drop=FALSE] ##change

-    temp_df<-as.data.frame(colData(SCE)[,c(aggregateCol),drop=FALSE]) %>% unite("new_colnames",1:ncol(.),sep = "_") %>% remove_rownames() %>% column_to_rownames("new_colnames")

+    

+    temp_df<-as.data.frame(colData(SCE)[,c(aggregateCol),drop=FALSE]) %>% 

+      unite("new_colnames",1:ncol(.),sep = "_",remove = FALSE) %>% 

+      remove_rownames() %>% 

+      mutate(aggregated_column = new_colnames) %>%

+      dplyr::select(new_colnames, aggregated_column) %>%

+      column_to_rownames("new_colnames")

+

     colData(SCE)<-DataFrame(temp_df)

     rowData(SCE) <- origRowData

   }

@@ -278,14 +300,14 @@ plotSCEHeatmap <- function(inSCE, useAssay = 'logcounts', useReducedDim = NULL,

     colData(SCE) <- origColData

   }

   # STAGE 4: Other minor preparation for plotting ####

-

+ 

   # Create a function that sorts the matrix by PC1

   .orderMatrix<-function(mat){

     # Adding extra character to rownames because presence of some char gets a "." if I don't

     mat2<-data.frame(t(mat))

     rownames(mat2)<-stringr::str_c("K_",rownames(mat2))

     pca_mat<-stats::prcomp(mat2,center = TRUE, scale. = FALSE)

-    kl<-dplyr::arrange(data.frame(pca_mat$x)["PC1"],desc(PC1))

+    kl<-dplyr::arrange(data.frame(pca_mat$x)["PC1"],desc(data.frame(pca_mat$x)["PC1"]))

     mat<-data.frame(t(mat2)) %>% dplyr::select(rownames(kl))

     colnames(mat)<-stringr::str_replace_all(colnames(mat),"K_","")

     return(as.matrix(mat))

@@ -298,10 +320,15 @@ plotSCEHeatmap <- function(inSCE, useAssay = 'logcounts', useReducedDim = NULL,

     mat <- .orderMatrix(mat)

   } else{

-    mat<- assay(SCE)

+    

+    if(class(assay(SCE))[1] == "dgCMatrix"){

+      mat<- as.matrix(assay(SCE))

+    }

+    else{

+     mat <- assay(SCE)

+    }

   }

- 

   if (!is.null(trim) & scale == "zscore") {

     assay(SCE) <- trimCounts(assay(SCE), trim)  

@@ -344,6 +371,8 @@ plotSCEHeatmap <- function(inSCE, useAssay = 'logcounts', useReducedDim = NULL,

     if (breaks[1] != min(trim) || breaks[length(breaks)] != max(trim))

       stop('Breaks of `colorScheme` do not match with `trim`.')

   }

+  

+  

   ### Generate HeatmapAnnotation object

   ca <- NULL

   cellAnnotationColor <- .heatmapAnnColor(SCE, slot = "colData",

@@ -351,7 +380,7 @@ plotSCEHeatmap <- function(inSCE, useAssay = 'logcounts', useReducedDim = NULL,

                                           palette = palette)

   if(dim(cellAnnotations)[2] > 0)

     if(is.null(addCellSummary)){

-      ca <- ComplexHeatmap::HeatmapAnnotation(df = colData(SCE),

+      ca <- ComplexHeatmap::HeatmapAnnotation(df = as.data.frame(colData(SCE)),

                                               col = cellAnnotationColor)

     }

   else if (!addCellSummary %in% colnames(oldColData)){

@@ -415,6 +444,7 @@ plotSCEHeatmap <- function(inSCE, useAssay = 'logcounts', useReducedDim = NULL,

                                 show_row_names = rowLabel,

                                 row_names_gp = grid::gpar(fontsize = rowLabelSize),

                                 show_row_dend = rowDend,

+                                show_column_dend = colDend,

                                 row_dend_reorder = TRUE,

                                 cluster_columns = FALSE,

                                 show_column_names = colLabel,