@@ -16,9 +16,11 @@

 #'  \linkS4class{SingleCellExperiment} object. Default "counts".

 #' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

-#' @param featureModule Integer Vector. The featureModule(s) to display.

+#' @param modules Integer Vector. The featureModule(s) to display.

 #'  Multiple modules can be included in a vector. Default \code{NULL} which

 #'  plots all module heatmaps.

+#' @param featureModule Same as \code{modules}. Either can be used to specify

+#' the modules to display. 

 #' @param col Passed to \link[ComplexHeatmap]{Heatmap}. Set color boundaries

 #'  and colors.

 #' @param topCells Integer. Number of cells with the highest and lowest

@@ -100,6 +102,9 @@

 #' and reduced the memory of the plot and the size of a file. If \code{NULL},

 #' then rasterization will be automatically determined by the underlying

 #' \link[ComplexHeatmap]{Heatmap} function. Default \code{TRUE}.

+#' @param returnAsList Boolean. If \code{TRUE}, then a list of plots will be

+#' returned instead of a single multi-panel figure. These plots can be 

+#' displayed using the \link[grid]{grid.draw} function. Default \code{FALSE}.

 #' @param ... Additional parameters passed to \link[ComplexHeatmap]{Heatmap}.

 #' @return A \link[multipanelfigure]{multi_panel_figure} object if plotting

 #'  more than one module heatmaps. Otherwise a

@@ -111,6 +116,7 @@ setGeneric("moduleHeatmap",

     function(x,

         useAssay = "counts",

         altExpName = "featureSubset",

+        modules = NULL,        

         featureModule = NULL,

         col = circlize::colorRamp2(c(-2, 0, 2),

             c("#1E90FF", "#FFFFFF", "#CD2626")),

@@ -136,6 +142,7 @@ setGeneric("moduleHeatmap",

         unit = "mm",

         ncol = NULL,

         useRaster = TRUE,

+        returnAsList = FALSE,

         ...) {

     standardGeneric("moduleHeatmap")})

@@ -151,6 +158,7 @@ setMethod("moduleHeatmap",

     function(x,

         useAssay = "counts",

         altExpName = "featureSubset",

+        modules = NULL,

         featureModule = NULL,

         col = circlize::colorRamp2(c(-2, 0, 2),

             c("#1E90FF", "#FFFFFF", "#CD2626")),

@@ -176,8 +184,15 @@ setMethod("moduleHeatmap",

         unit = "mm",

         ncol = NULL,

         useRaster = TRUE,

+        returnAsList = FALSE,

         ...) {

+        # 'modules' is an easier parameter name to remember so we include 

+        # support for both. 

+        if(!is.null(modules)) {

+            featureModule <- modules

+        }

+        

         altExp <- SingleCellExperiment::altExp(x, altExpName)

         counts <- SummarizedExperiment::assay(altExp, i = useAssay)

@@ -212,6 +227,8 @@ setMethod("moduleHeatmap",

         if (moduleLabel == "auto") {

             moduleLabel <- paste0("Module ", as.character(featureModule))

+        } else if (length(moduleLabel) == 1 & length(featureModule) > 1) {

+            moduleLabel <- rep(moduleLabel, length(featureModule))

         } else if (length(moduleLabel) != length(featureModule)) {

             stop("Invalid 'moduleLabel' length")

         }

@@ -264,12 +281,20 @@ setMethod("moduleHeatmap",

         # Get max rowFontSize if multiple modules are selected

         if (is.null(rowFontSize)) {

-          if (length(featureIndices) > 1) {

+          if (length(featureIndices) > 1 & !isTRUE(returnAsList)) {

+            # If there is more than 1 module selected, then the miniumum size

+            # size will be caculated for each module. This will ensure that

+            # all modules will have the same rowFontSize and the module

+            # heatmaps will have the same width. 

             maxlen <- max(unlist(lapply(featureIndices, length)))

             maxlen <- maxlen * sqrt(length(featureIndices))

-            rowFontSize <- min(200 / maxlen, 20)

+            rowFontSize <- rep(min(200 / maxlen, 20), length(featureIndices))

           } else {

-            rowFontSize <- min(200 / length(featureIndices[[1]]), 20)

+            # If there is only one plot or each plot will be generated 

+            # separately and returned in a list, then the size of the labels,

+            # will be caculated for each module separately.

+            len <- unlist(lapply(featureIndices, length))

+            rowFontSize <- pmin(200 / len, 20)

           }

         }

@@ -288,7 +313,7 @@ setMethod("moduleHeatmap",

                 showFeatureNames = showFeatureNames,

                 displayNames = displayNames[featureIndices[[i]]],

                 trim = trim,

-                rowFontSize = rowFontSize,

+                rowFontSize = rowFontSize[i],

                 showHeatmapLegend = showHeatmapLegend,

                 showTopAnnotationLegend = showTopAnnotationLegend,

                 showTopAnnotationName = showTopAnnotationName,

@@ -315,17 +340,22 @@ setMethod("moduleHeatmap",

                     wrap.grobs = TRUE)

             }

-            figure <- multipanelfigure::multi_panel_figure(

-                columns = ncol,

-                rows = nrow,

-                width = width,

-                height = height,

-                unit = unit)

-

-            for (i in seq(length(plts))) {

-                figure <- suppressMessages(multipanelfigure::fill_panel(figure,

-                    plts[[i]], label = ""))

+            if(isTRUE(returnAsList)) {

+                figure <- plts    

+            } else {

+                figure <- multipanelfigure::multi_panel_figure(

+                    columns = ncol,

+                    rows = nrow,

+                    width = width,

+                    height = height,

+                    unit = unit)

+                

+                for (i in seq(length(plts))) {

+                    figure <- suppressMessages(multipanelfigure::fill_panel(figure,

+                                                                            plts[[i]], label = ""))

+                }

             }

+            

             suppressWarnings(return(figure))

         }

     }

@@ -410,6 +440,10 @@ setMethod("moduleHeatmap",

         } else {

             stop("'scaleRow' needs to be of class 'function'")

         }

+        # If the standard deviation was 0 then the values will be NA

+        # Replacing the NAs with zero will keep the row the middle color

+        # rather than grey (default with ComplexHeatmap)

+        filteredNormCounts[is.na(filteredNormCounts)] <- 0

     }

     if (!is.null(trim)) {

@@ -264,7 +264,7 @@ setMethod("moduleHeatmap",

         # Get max rowFontSize if multiple modules are selected

         if (is.null(rowFontSize)) {

-          if(length(featureIndices) > 1) {

+          if (length(featureIndices) > 1) {

             maxlen <- max(unlist(lapply(featureIndices, length)))

             maxlen <- maxlen * sqrt(length(featureIndices))

             rowFontSize <- min(200 / maxlen, 20)

@@ -272,7 +272,7 @@ setMethod("moduleHeatmap",

             rowFontSize <- min(200 / length(featureIndices[[1]]), 20)

           }

         }

-        

+

         plts <- vector("list", length = length(featureModule))

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

             plts[[i]] <- .plotModuleHeatmap(normCounts = normCounts,

@@ -251,6 +251,7 @@ setMethod("moduleHeatmap",

             }

         )

+        # Set up displayName variable if specified

         if (is.null(displayName)) {

             displayNames <- rownames(altExp)

         } else {

@@ -261,8 +262,18 @@ setMethod("moduleHeatmap",

         z <- celdaClusters(x, altExpName = altExpName)

         y <- celdaModules(x, altExpName = altExpName)

+        # Get max rowFontSize if multiple modules are selected

+        if (is.null(rowFontSize)) {

+          if(length(featureIndices) > 1) {

+            maxlen <- max(unlist(lapply(featureIndices, length)))

+            maxlen <- maxlen * sqrt(length(featureIndices))

+            rowFontSize <- min(200 / maxlen, 20)

+          } else {

+            rowFontSize <- min(200 / length(featureIndices[[1]]), 20)

+          }

+        }

+        

         plts <- vector("list", length = length(featureModule))

-

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

             plts[[i]] <- .plotModuleHeatmap(normCounts = normCounts,

                 col = col,

@@ -413,10 +424,6 @@ setMethod("moduleHeatmap",

         filteredNormCounts[filteredNormCounts > trim[2]] <- trim[2]

     }

-    if (is.null(rowFontSize)) {

-        rowFontSize <- min(200 / nrow(filteredNormCounts), 20)

-    }

-

     if (isTRUE(showModuleLabel)) {

         plt <- ComplexHeatmap::Heatmap(matrix = filteredNormCounts,

             col = col,

@@ -369,9 +369,10 @@ setMethod("moduleHeatmap",

     filteredNormCounts <-

         normCounts[featureIndices, cellIndices, drop = FALSE]

-    filteredNormCounts <-

-        filteredNormCounts[rowSums(filteredNormCounts > 0) > 0, ,

-            drop = FALSE]

+    # Show/hide features with 0 counts in these cells in the module

+    # filteredNormCounts <-

+    #     filteredNormCounts[rowSums(filteredNormCounts > 0) > 0, ,

+    #         drop = FALSE]

     geneIx <- match(rownames(filteredNormCounts), rownames(normCounts))

     cellIx <- match(colnames(filteredNormCounts), colnames(normCounts))

@@ -420,7 +421,7 @@ setMethod("moduleHeatmap",

         plt <- ComplexHeatmap::Heatmap(matrix = filteredNormCounts,

             col = col,

             row_title = moduleLabel,

-            row_title_gp = gpar(fontsize = moduleLabelSize),

+            row_title_gp = grid::gpar(fontsize = moduleLabelSize),

             show_column_names = FALSE,

             show_row_names = showFeatureNames,

             row_labels = displayNames,

@@ -107,7 +107,36 @@

 #' @importFrom methods .hasSlot

 #' @importFrom multipanelfigure multi_panel_figure

 #' @export

-setGeneric("moduleHeatmap", function(x, ...) {

+setGeneric("moduleHeatmap",

+    function(x,

+        useAssay = "counts",

+        altExpName = "featureSubset",

+        featureModule = NULL,

+        col = circlize::colorRamp2(c(-2, 0, 2),

+            c("#1E90FF", "#FFFFFF", "#CD2626")),

+        topCells = 100,

+        topFeatures = NULL,

+        normalizedCounts = NA,

+        normalize = "proportion",

+        transformationFun = sqrt,

+        scaleRow = scale,

+        showFeatureNames = TRUE,

+        displayName = NULL,

+        trim = c(-2, 2),

+        rowFontSize = NULL,

+        showHeatmapLegend = FALSE,

+        showTopAnnotationLegend = FALSE,

+        showTopAnnotationName = FALSE,

+        topAnnotationHeight = 5,

+        showModuleLabel = TRUE,

+        moduleLabel = "auto",

+        moduleLabelSize = NULL,

+        width = "auto",

+        height = "auto",

+        unit = "mm",

+        ncol = NULL,

+        useRaster = TRUE,

+        ...) {

     standardGeneric("moduleHeatmap")})

@@ -9,7 +9,8 @@

 #' @param x A numeric \link{matrix} of counts or a

 #'  \linkS4class{SingleCellExperiment}

 #'  with the matrix located in the assay slot under \code{useAssay}.

-#'  Rows represent features and columns represent cells.

+#'  Rows represent features and columns represent cells. Celda

+#'  results must be present under \code{metadata(altExp(x, altExpName))}.

 #' @param useAssay A string specifying which \link{assay}

 #'  slot to use if \code{x} is a

 #'  \linkS4class{SingleCellExperiment} object. Default "counts".

@@ -52,16 +53,21 @@

 #'  divides the library size of each cell by the mean library size across all

 #'  cells. Default "proportion".

 #' @param transformationFun Function. Passed to \link{normalizeCounts} if

-#'  \code{normalizedCounts} is \code{NA}. Applys a transformation such as

+#'  \code{normalizedCounts} is \code{NA}. Applies a transformation such as

 #'  \link{sqrt}, \link{log}, \link{log2}, \link{log10}, or \link{log1p}.

-#'  If NULL, no transformation will be applied. Occurs after normalization.

-#'  Default \link{sqrt}.

+#'  If \code{NULL}, no transformation will be applied. Occurs after

+#'  normalization. Default \link{sqrt}.

 #' @param scaleRow Function. Which function to use to scale each individual

 #'  row. Set to NULL to disable. Occurs after normalization and log

 #'  transformation. For example, \link{scale} will Z-score transform each row.

 #'  Default \link{scale}.

-#' @param showFeaturenames Logical. Wheter feature names should be displayed.

+#' @param showFeaturenames Logical. Whether feature names should be displayed.

 #'  Default TRUE.

+#' @param displayName Character. The column name of

+#'  \code{rowData(altExp(x, altExpName))} that specifies the display names for

+#'  the features. Default \code{NULL}, which displays the row names. Only works

+#'  if \code{showFeaturenames} is \code{TRUE} and \code{x} is a

+#'  \linkS4class{SingleCellExperiment} object.

 #' @param trim Numeric vector. Vector of length two that specifies the lower

 #'  and upper bounds for plotting the data. This threshold is applied

 #'  after row scaling. Set to NULL to disable. Default \code{c(-2,2)}.

@@ -108,7 +114,8 @@ setGeneric("moduleHeatmap", function(x, ...) {

 #' @rdname moduleHeatmap

 #' @examples

 #' data(sceCeldaCG)

-#' moduleHeatmap(sceCeldaCG, width = 250, height = 250)

+#' moduleHeatmap(sceCeldaCG, width = 250, height = 250,

+#'  displayName = "rownames")

 #' @export

 setMethod("moduleHeatmap",

     signature(x = "SingleCellExperiment"),

@@ -125,6 +132,7 @@ setMethod("moduleHeatmap",

         transformationFun = sqrt,

         scaleRow = scale,

         showFeaturenames = TRUE,

+        displayName = NULL,

         trim = c(-2, 2),

         rowFontSize = NULL,

         showHeatmapLegend = FALSE,

@@ -214,6 +222,13 @@ setMethod("moduleHeatmap",

             }

         )

+        if (is.null(displayName)) {

+            displayNames <- rownames(altExp)

+        } else {

+            displayNames <- SummarizedExperiment::rowData(altExp)[[

+                displayName]]

+        }

+

         z <- celdaClusters(x, altExpName = altExpName)

         y <- celdaModules(x, altExpName = altExpName)

@@ -231,6 +246,7 @@ setMethod("moduleHeatmap",

                 altExpName = altExpName,

                 scaleRow = scaleRow,

                 showFeaturenames = showFeaturenames,

+                displayNames = displayNames[featureIndices[[i]]],

                 trim = trim,

                 rowFontSize = rowFontSize,

                 showHeatmapLegend = showHeatmapLegend,

@@ -287,6 +303,7 @@ setMethod("moduleHeatmap",

     altExpName,

     scaleRow,

     showFeaturenames,

+    displayNames,

     trim,

     rowFontSize,

     showHeatmapLegend,

@@ -373,6 +390,7 @@ setMethod("moduleHeatmap",

             row_title_gp = gpar(fontsize = moduleLabelSize),

             show_column_names = FALSE,

             show_row_names = showFeaturenames,

+            row_labels = displayNames,

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

             cluster_rows = FALSE,

             cluster_columns = FALSE,

@@ -394,6 +412,7 @@ setMethod("moduleHeatmap",

             col = col,

             show_column_names = FALSE,

             show_row_names = showFeaturenames,

+            row_labels = displayNames,

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

             cluster_rows = FALSE,

             cluster_columns = FALSE,

@@ -366,10 +366,10 @@ setMethod("moduleHeatmap",

         filteredNormCounts[filteredNormCounts > trim[2]] <- trim[2]

     }

-    if(is.null(rowFontSize)) {

+    if (is.null(rowFontSize)) {

         rowFontSize <- min(200 / nrow(filteredNormCounts), 20)

     }

-    

+

     if (isTRUE(showModuleLabel)) {

         plt <- ComplexHeatmap::Heatmap(matrix = filteredNormCounts,

             col = col,

@@ -60,12 +60,12 @@

 #'  row. Set to NULL to disable. Occurs after normalization and log

 #'  transformation. For example, \link{scale} will Z-score transform each row.

 #'  Default \link{scale}.

-#' @param showFeaturenames Logical. Wheter feature names should be displayed.

+#' @param showFeatureNames Logical. Whether feature names should be displayed.

 #'  Default TRUE.

 #' @param trim Numeric vector. Vector of length two that specifies the lower

 #'  and upper bounds for plotting the data. This threshold is applied

 #'  after row scaling. Set to NULL to disable. Default \code{c(-2,2)}.

-#' @param rowFontSize Integer. Font size for feature names. If \code{NULL},

+#' @param rowFontSize Numeric. Font size for feature names. If \code{NULL},

 #' then the size will automatically be determined. Default \code{NULL}.

 #' @param showHeatmapLegend Passed to \link[ComplexHeatmap]{Heatmap}. Show

 #'  legend for expression levels.

@@ -124,7 +124,7 @@ setMethod("moduleHeatmap",

         normalize = "proportion",

         transformationFun = sqrt,

         scaleRow = scale,

-        showFeaturenames = TRUE,

+        showFeatureNames = TRUE,

         trim = c(-2, 2),

         rowFontSize = NULL,

         showHeatmapLegend = FALSE,

@@ -230,7 +230,7 @@ setMethod("moduleHeatmap",

                 topCells = topCells,

                 altExpName = altExpName,

                 scaleRow = scaleRow,

-                showFeaturenames = showFeaturenames,

+                showFeatureNames = showFeatureNames,

                 trim = trim,

                 rowFontSize = rowFontSize,

                 showHeatmapLegend = showHeatmapLegend,

@@ -286,7 +286,7 @@ setMethod("moduleHeatmap",

     topCells,

     altExpName,

     scaleRow,

-    showFeaturenames,

+    showFeatureNames,

     trim,

     rowFontSize,

     showHeatmapLegend,

@@ -366,13 +366,17 @@ setMethod("moduleHeatmap",

         filteredNormCounts[filteredNormCounts > trim[2]] <- trim[2]

     }

+    if(is.null(rowFontSize)) {

+        rowFontSize <- min(200 / nrow(filteredNormCounts), 20)

+    }

+    

     if (isTRUE(showModuleLabel)) {

         plt <- ComplexHeatmap::Heatmap(matrix = filteredNormCounts,

             col = col,

             row_title = moduleLabel,

             row_title_gp = gpar(fontsize = moduleLabelSize),

             show_column_names = FALSE,

-            show_row_names = showFeaturenames,

+            show_row_names = showFeatureNames,

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

             cluster_rows = FALSE,

             cluster_columns = FALSE,

@@ -393,7 +397,7 @@ setMethod("moduleHeatmap",

         plt <- ComplexHeatmap::Heatmap(matrix = filteredNormCounts,

             col = col,

             show_column_names = FALSE,

-            show_row_names = showFeaturenames,

+            show_row_names = showFeatureNames,

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

             cluster_rows = FALSE,

             cluster_columns = FALSE,

@@ -87,6 +87,9 @@

 #'  height of the output figure.

 #' @param unit Passed to \link[multipanelfigure]{multi_panel_figure}. Single

 #'  character object defining the unit of all dimensions defined.

+#' @param ncol Integer. Number of columns of module heatmaps. If \code{NULL},

+#' then this will be automatically calculated so that the number of columns

+#' and rows will be approximately the same. Default \code{NULL}.

 #' @param useRaster Boolean. Rasterizing will make the heatmap a single object

 #' and reduced the memory of the plot and the size of a file. If \code{NULL},

 #' then rasterization will be automatically determined by the underlying

@@ -134,6 +137,7 @@ setMethod("moduleHeatmap",

         width = "auto",

         height = "auto",

         unit = "mm",

+        ncol = NULL,

         useRaster = TRUE,

         ...) {

@@ -244,7 +248,9 @@ setMethod("moduleHeatmap",

         if (isTRUE(returnHeatmap)) {

             return(plts[[1]])

         } else {

-            ncol <- floor(sqrt(length(plts)))

+            if (is.null(ncol)) {

+              ncol <- floor(sqrt(length(plts)))

+            }

             nrow <- ceiling(length(plts) / ncol)

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

@@ -253,7 +259,8 @@ setMethod("moduleHeatmap",

                     wrap.grobs = TRUE)

             }

-            figure <- multipanelfigure::multi_panel_figure(columns = ncol,

+            figure <- multipanelfigure::multi_panel_figure(

+                columns = ncol,

                 rows = nrow,

                 width = width,

                 height = height,

@@ -90,7 +90,7 @@

 #' @param useRaster Boolean. Rasterizing will make the heatmap a single object

 #' and reduced the memory of the plot and the size of a file. If \code{NULL},

 #' then rasterization will be automatically determined by the underlying

-#' \link[ComplexHeatmap]{Heatmap} function. Default \code{TRUE}. 

+#' \link[ComplexHeatmap]{Heatmap} function. Default \code{TRUE}.

 #' @param ... Additional parameters passed to \link[ComplexHeatmap]{Heatmap}.

 #' @return A \link[multipanelfigure]{multi_panel_figure} object if plotting

 #'  more than one module heatmaps. Otherwise a

@@ -64,8 +64,9 @@

 #'  Default TRUE.

 #' @param trim Numeric vector. Vector of length two that specifies the lower

 #'  and upper bounds for plotting the data. This threshold is applied

-#'  after row scaling. Set to NULL to disable. Default c(-2,2).

-#' @param rowFontSize Integer. Font size for genes.

+#'  after row scaling. Set to NULL to disable. Default \code{c(-2,2)}.

+#' @param rowFontSize Integer. Font size for feature names. If \code{NULL},

+#' then the size will automatically be determined. Default \code{NULL}.

 #' @param showHeatmapLegend Passed to \link[ComplexHeatmap]{Heatmap}. Show

 #'  legend for expression levels.

 #' @param showTopAnnotationLegend Passed to

@@ -122,14 +123,14 @@ setMethod("moduleHeatmap",

         scaleRow = scale,

         showFeaturenames = TRUE,

         trim = c(-2, 2),

-        rowFontSize = 6,

+        rowFontSize = NULL,

         showHeatmapLegend = FALSE,

         showTopAnnotationLegend = FALSE,

         showTopAnnotationName = FALSE,

-        topAnnotationHeight = 1.5,

+        topAnnotationHeight = 5,

         showModuleLabel = TRUE,

         moduleLabel = "auto",

-        moduleLabelSize = 13,

+        moduleLabelSize = NULL,

         width = "auto",

         height = "auto",

         unit = "mm",

@@ -170,9 +171,8 @@ setMethod("moduleHeatmap",

         if (moduleLabel == "auto") {

             moduleLabel <- paste0("Module ", as.character(featureModule))

-        } else if (length(moduleLabel) != length(unique(celdaModules(x,

-            altExpName = altExpName)))) {

-            stop("Invalid 'moduleLabel' length!")

+        } else if (length(moduleLabel) != length(featureModule)) {

+            stop("Invalid 'moduleLabel' length")

         }

         # factorize counts matrix

@@ -379,7 +379,8 @@ setMethod("moduleHeatmap",

                 show_legend = showTopAnnotationLegend,

                 show_annotation_name = showTopAnnotationName,

                 col = list(cell = ccols),

-                simple_anno_size = grid::unit(topAnnotationHeight, unit)),

+                simple_anno_size = grid::unit(topAnnotationHeight, unit),

+                simple_anno_size_adjust = TRUE),

             ...)

     } else {

         plt <- ComplexHeatmap::Heatmap(matrix = filteredNormCounts,

@@ -399,7 +400,8 @@ setMethod("moduleHeatmap",

                 show_legend = showTopAnnotationLegend,

                 show_annotation_name = showTopAnnotationName,

                 col = list(cell = ccols),

-                simple_anno_size = grid::unit(topAnnotationHeight, unit)),

+                simple_anno_size = grid::unit(topAnnotationHeight, unit),

+                simple_anno_size_adjust = TRUE),

             ...)

     }

     return(plt)

@@ -86,6 +86,10 @@

 #'  height of the output figure.

 #' @param unit Passed to \link[multipanelfigure]{multi_panel_figure}. Single

 #'  character object defining the unit of all dimensions defined.

+#' @param useRaster Boolean. Rasterizing will make the heatmap a single object

+#' and reduced the memory of the plot and the size of a file. If \code{NULL},

+#' then rasterization will be automatically determined by the underlying

+#' \link[ComplexHeatmap]{Heatmap} function. Default \code{TRUE}. 

 #' @param ... Additional parameters passed to \link[ComplexHeatmap]{Heatmap}.

 #' @return A \link[multipanelfigure]{multi_panel_figure} object if plotting

 #'  more than one module heatmaps. Otherwise a

@@ -129,6 +133,7 @@ setMethod("moduleHeatmap",

         width = "auto",

         height = "auto",

         unit = "mm",

+        useRaster = TRUE,

         ...) {

         altExp <- SingleCellExperiment::altExp(x, altExpName)

@@ -231,6 +236,7 @@ setMethod("moduleHeatmap",

                 showModuleLabel = showModuleLabel,

                 moduleLabel = moduleLabel[i],

                 moduleLabelSize = moduleLabelSize,

+                useRaster = useRaster,

                 unit = unit,

                 ... = ...)

         }

@@ -283,6 +289,7 @@ setMethod("moduleHeatmap",

     showModuleLabel,

     moduleLabel,

     moduleLabelSize,

+    useRaster,

     unit,

     ...) {

@@ -364,6 +371,7 @@ setMethod("moduleHeatmap",

             cluster_columns = FALSE,

             heatmap_legend_param = list(title = "Expression"),

             show_heatmap_legend = showHeatmapLegend,

+            use_raster = useRaster,

             top_annotation = ComplexHeatmap::HeatmapAnnotation(

                 cell = factor(zToPlot,

                     levels = stringr::str_sort(unique(zToPlot),

@@ -383,6 +391,7 @@ setMethod("moduleHeatmap",

             cluster_columns = FALSE,

             heatmap_legend_param = list(title = "Expression"),

             show_heatmap_legend = showHeatmapLegend,

+            use_raster = useRaster,

             top_annotation = ComplexHeatmap::HeatmapAnnotation(

                 cell = factor(zToPlot,

                     levels = stringr::str_sort(unique(zToPlot),

@@ -242,7 +242,8 @@ setMethod("moduleHeatmap",

             nrow <- ceiling(length(plts) / ncol)

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

-                plts[[i]] <- grid::grid.grabExpr(ComplexHeatmap::draw(plts[[i]]),

+                plts[[i]] <- grid::grid.grabExpr(

+                    ComplexHeatmap::draw(plts[[i]]),

                     wrap.grobs = TRUE)

             }

@@ -87,7 +87,9 @@

 #' @param unit Passed to \link[multipanelfigure]{multi_panel_figure}. Single

 #'  character object defining the unit of all dimensions defined.

 #' @param ... Additional parameters passed to \link[ComplexHeatmap]{Heatmap}.

-#' @return A \link[multipanelfigure]{multi_panel_figure} object.

+#' @return A \link[multipanelfigure]{multi_panel_figure} object if plotting

+#'  more than one module heatmaps. Otherwise a

+#'  \link[ComplexHeatmap]{HeatmapList} object is returned.

 #' @importFrom methods .hasSlot

 #' @importFrom multipanelfigure multi_panel_figure

 #' @export

@@ -155,6 +157,12 @@ setMethod("moduleHeatmap",

             featureModule <- sort(unique(celdaModules(x)))

         }

+        if (length(featureModule) == 1) {

+            returnHeatmap <- TRUE

+        } else {

+            returnHeatmap <- FALSE

+        }

+

         if (moduleLabel == "auto") {

             moduleLabel <- paste0("Module ", as.character(featureModule))

         } else if (length(moduleLabel) != length(unique(celdaModules(x,

@@ -227,25 +235,29 @@ setMethod("moduleHeatmap",

                 ... = ...)

         }

-        ncol <- floor(sqrt(length(plts)))

-        nrow <- ceiling(length(plts) / ncol)

+        if (isTRUE(returnHeatmap)) {

+            return(plts[[1]])

+        } else {

+            ncol <- floor(sqrt(length(plts)))

+            nrow <- ceiling(length(plts) / ncol)

-        for (i in seq(length(plts))) {

-            plts[[i]] <- grid::grid.grabExpr(ComplexHeatmap::draw(plts[[i]]),

-                wrap.grobs = TRUE)

-        }

+            for (i in seq(length(plts))) {

+                plts[[i]] <- grid::grid.grabExpr(ComplexHeatmap::draw(plts[[i]]),

+                    wrap.grobs = TRUE)

+            }

-        figure <- multipanelfigure::multi_panel_figure(columns = ncol,

-            rows = nrow,

-            width = width,

-            height = height,

-            unit = unit)

+            figure <- multipanelfigure::multi_panel_figure(columns = ncol,

+                rows = nrow,

+                width = width,

+                height = height,

+                unit = unit)

-        for (i in seq(length(plts))) {

-            figure <- suppressMessages(multipanelfigure::fill_panel(figure,

-                plts[[i]], label = ""))

+            for (i in seq(length(plts))) {

+                figure <- suppressMessages(multipanelfigure::fill_panel(figure,

+                    plts[[i]], label = ""))

+            }

+            suppressWarnings(return(figure))

         }

-        suppressWarnings(return(figure))

     }

 )

@@ -72,29 +72,20 @@

 #'  \link[ComplexHeatmap]{HeatmapAnnotation}. Show legend for cell annotation.

 #' @param showTopAnnotationName Passed to

 #'  \link[ComplexHeatmap]{HeatmapAnnotation}. Show heatmap top annotation name.

-#' @param showLeftAnnotationLegend Passed to

-#'  \link[ComplexHeatmap]{HeatmapAnnotation}. Show legend for feature module

-#'  annotation.

 #' @param topAnnotationHeight Passed to

 #'  \link[ComplexHeatmap]{HeatmapAnnotation}. Column annotation height.

 #'  \link[ComplexHeatmap]{rowAnnotation}. Show legend for module annotation.

-#' @param showLeftAnnotation Show left annotation. Default \code{FALSE}.

-#' @param showLeftAnnotationName Passed to

-#'  \link[ComplexHeatmap]{rowAnnotation}. Show heatmap left annotation name.

-#' @param leftAnnotationWidth Passed to

-#'  \link[ComplexHeatmap]{rowAnnotation}. Row annotation width.

+#' @param showModuleLabel Show left side module labels.

+#' @param moduleLabel The left side row titles for module heatmap. Must be

+#'  vector of the same length as \code{featureModule}. Default "auto", which

+#'  automatically pulls module labels from \code{x}.

+#' @param moduleLabelSize Passed to \link{gpar}. The size of text (in points).

 #' @param width Passed to \link[multipanelfigure]{multi_panel_figure}. The

 #'  width of the output figure.

 #' @param height Passed to \link[multipanelfigure]{multi_panel_figure}. The

 #'  height of the output figure.

 #' @param unit Passed to \link[multipanelfigure]{multi_panel_figure}. Single

 #'  character object defining the unit of all dimensions defined.

-#' @param ModuleLabel Must be

-#'  vector of the same length as \code{length(unique(celdaModules(x)))} or

-#'  \code{length(unique(celdaClusters(x)$y))}. Set to \code{""} to disable.

-#' @param labelJust Passed to \link[multipanelfigure]{fill_panel}.

-#'  Justification for the label within the interpanel spacing grob to the

-#'  top-left of the panel content grob.

 #' @param ... Additional parameters passed to \link[ComplexHeatmap]{Heatmap}.

 #' @return A \link[multipanelfigure]{multi_panel_figure} object.

 #' @importFrom methods .hasSlot

@@ -130,15 +121,12 @@ setMethod("moduleHeatmap",

         showTopAnnotationLegend = FALSE,

         showTopAnnotationName = FALSE,

         topAnnotationHeight = 1.5,

-        showLeftAnnotation = FALSE,

-        showLeftAnnotationLegend = FALSE,

-        showLeftAnnotationName = FALSE,

-        leftAnnotationWidth = 1.5,

+        showModuleLabel = TRUE,

+        moduleLabel = "auto",

+        moduleLabelSize = 13,

         width = "auto",

         height = "auto",

         unit = "mm",

-        ModuleLabel = "auto",

-        labelJust = c("right", "bottom"),

         ...) {

         altExp <- SingleCellExperiment::altExp(x, altExpName)

@@ -167,16 +155,11 @@ setMethod("moduleHeatmap",

             featureModule <- sort(unique(celdaModules(x)))

         }

-        if (is.null(ModuleLabel)) {

-            ModuleLabel <- NULL

-        } else if (ModuleLabel == "auto") {

-            ModuleLabel <- as.character(featureModule)

-        } else if (ModuleLabel == "") {

-            ModuleLabel <- rep("", length = length(unique(celdaModules(x,

-                altExpName = altExpName))))

-        } else if (length(ModuleLabel) != length(unique(celdaModules(x,

+        if (moduleLabel == "auto") {

+            moduleLabel <- paste0("Module ", as.character(featureModule))

+        } else if (length(moduleLabel) != length(unique(celdaModules(x,

             altExpName = altExpName)))) {

-            stop("Invalid 'ModuleLabel' length!")

+            stop("Invalid 'moduleLabel' length!")

         }

         # factorize counts matrix

@@ -237,15 +220,13 @@ setMethod("moduleHeatmap",

                 showTopAnnotationLegend = showTopAnnotationLegend,

                 showTopAnnotationName = showTopAnnotationName,

                 topAnnotationHeight = topAnnotationHeight,

-                showLeftAnnotation = showLeftAnnotation,

-                showLeftAnnotationLegend = showLeftAnnotationLegend,

-                showLeftAnnotationName = showLeftAnnotationName,

-                leftAnnotationWidth = leftAnnotationWidth,

+                showModuleLabel = showModuleLabel,

+                moduleLabel = moduleLabel[i],

+                moduleLabelSize = moduleLabelSize,

                 unit = unit,

                 ... = ...)

         }

-

         ncol <- floor(sqrt(length(plts)))

         nrow <- ceiling(length(plts) / ncol)

@@ -261,13 +242,8 @@ setMethod("moduleHeatmap",

             unit = unit)

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

-            if (!is.null(ModuleLabel)) {

-                figure <- suppressMessages(multipanelfigure::fill_panel(figure,

-                    plts[[i]], label = ModuleLabel[i], label_just = labelJust))

-            } else {

-                figure <- suppressMessages(multipanelfigure::fill_panel(figure,

-                    plts[[i]], label_just = labelJust))

-            }

+            figure <- suppressMessages(multipanelfigure::fill_panel(figure,

+                plts[[i]], label = ""))

         }

         suppressWarnings(return(figure))

     }

@@ -291,10 +267,9 @@ setMethod("moduleHeatmap",

     showTopAnnotationLegend,

     showTopAnnotationName,

     topAnnotationHeight,

-    showLeftAnnotation,

-    showLeftAnnotationLegend,

-    showLeftAnnotationName,

-    leftAnnotationWidth,

+    showModuleLabel,

+    moduleLabel,

+    moduleLabelSize,

     unit,

     ...) {

@@ -364,9 +339,11 @@ setMethod("moduleHeatmap",

         filteredNormCounts[filteredNormCounts > trim[2]] <- trim[2]

     }

-    if (isTRUE(showLeftAnnotation)) {

+    if (isTRUE(showModuleLabel)) {

         plt <- ComplexHeatmap::Heatmap(matrix = filteredNormCounts,

             col = col,

+            row_title = moduleLabel,

+            row_title_gp = gpar(fontsize = moduleLabelSize),

             show_column_names = FALSE,

             show_row_names = showFeaturenames,

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

@@ -382,14 +359,6 @@ setMethod("moduleHeatmap",

                 show_annotation_name = showTopAnnotationName,

                 col = list(cell = ccols),

                 simple_anno_size = grid::unit(topAnnotationHeight, unit)),

-            left_annotation = ComplexHeatmap::rowAnnotation(

-                module = factor(yToPlot,

-                    levels = stringr::str_sort(unique(yToPlot),

-                        numeric = TRUE)),

-                show_legend = showLeftAnnotationLegend,

-                show_annotation_name = showLeftAnnotationName,

-                col = list(module = rcols),

-                simple_anno_size = grid::unit(leftAnnotationWidth, unit)),

             ...)

     } else {

         plt <- ComplexHeatmap::Heatmap(matrix = filteredNormCounts,

@@ -10,10 +10,10 @@

 #'  \linkS4class{SingleCellExperiment}

 #'  with the matrix located in the assay slot under \code{useAssay}.

 #'  Rows represent features and columns represent cells.

-#' @param useAssay A string specifying which \link[SummarizedExperiment]{assay}

+#' @param useAssay A string specifying which \link{assay}

 #'  slot to use if \code{x} is a

 #'  \linkS4class{SingleCellExperiment} object. Default "counts".

-#' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

+#' @param altExpName The name for the \link{altExp} slot

 #'  to use. Default "featureSubset".

 #' @param featureModule Integer Vector. The featureModule(s) to display.

 #'  Multiple modules can be included in a vector. Default \code{NULL} which

@@ -15,8 +15,6 @@

 #'  \linkS4class{SingleCellExperiment} object. Default "counts".

 #' @param altExpName The name for the \link[SingleCellExperiment]{altExp} slot

 #'  to use. Default "featureSubset".

-#' @param celdaMod Celda object of class \link{celda_G} or \link{celda_CG}. Used

-#'  only if \code{x} is a matrix object.

 #' @param featureModule Integer Vector. The featureModule(s) to display.

 #'  Multiple modules can be included in a vector. Default \code{NULL} which

 #'  plots all module heatmaps.