@@ -11,7 +11,7 @@

 #'  Rows represent features and columns represent cells. Alternatively,

 #'  any matrix-like object that can be coerced to a sparse matrix of class

 #'  "dgCMatrix" can be directly used as input. The matrix will automatically be

-#'  converted to a \linkS4class{SingleCellExperiment} object. 

+#'  converted to a \linkS4class{SingleCellExperiment} object.

 #' @param useAssay A string specifying the name of the

 #'  \link{assay} slot to use. Default "counts".

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

@@ -189,7 +189,7 @@ setMethod("celda_C",

         # Convert to sparse matrix

         x <- methods::as(x, "dgCMatrix")

-        

+

         ls <- list()

         ls[[useAssay]] <- x

         sce <- SingleCellExperiment::SingleCellExperiment(assays = ls)

@@ -11,7 +11,7 @@

 #'  Rows represent features and columns represent cells. Alternatively,

 #'  any matrix-like object that can be coerced to a sparse matrix of class

 #'  "dgCMatrix" can be directly used as input. The matrix will automatically be

-#'  converted to a \linkS4class{SingleCellExperiment} object. 

+#'  converted to a \linkS4class{SingleCellExperiment} object.

 #' @param useAssay A string specifying the name of the

 #'  \link{assay} slot to use. Default "counts".

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

@@ -223,7 +223,7 @@ setMethod("celda_CG",

         # Convert to sparse matrix

         x <- methods::as(x, "dgCMatrix")

-      

+

         ls <- list()

         ls[[useAssay]] <- x

         sce <- SingleCellExperiment::SingleCellExperiment(assays = ls)

@@ -11,7 +11,7 @@

 #'  Rows represent features and columns represent cells. Alternatively,

 #'  any matrix-like object that can be coerced to a sparse matrix of class

 #'  "dgCMatrix" can be directly used as input. The matrix will automatically be

-#'  converted to a \linkS4class{SingleCellExperiment} object. 

+#'  converted to a \linkS4class{SingleCellExperiment} object.

 #' @param useAssay A string specifying the name of the

 #'  \link{assay} slot to use. Default "counts".

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

@@ -173,7 +173,7 @@ setMethod("celda_G",

         # Convert to sparse matrix

         x <- methods::as(x, "dgCMatrix")

-      

+

         ls <- list()

         ls[[useAssay]] <- x

         sce <- SingleCellExperiment::SingleCellExperiment(assays = ls)

@@ -553,7 +553,7 @@ featureModuleTable <- function(sce,

       altExpName = altExpName,

       type = "proportion")

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

-  

+

   allGenes <- topRank(factorizeMatrix$proportions$module, n = nrow(altExp))

   maxlen <- max(vapply(allGenes$names, length, integer(1)))

@@ -44,14 +44,14 @@ setMethod("featureModuleLookup", signature(sce = "SingleCellExperiment"),

         by = "rownames") {

         modules <- as.numeric(celdaModules(sce, altExpName = altExpName))

-        

+

         if (celdaModel(sce, altExpName = altExpName) %in%

                 c("celda_CG", "celda_G")) {

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

           featureIndex <- retrieveFeatureIndex(features, x = altExp,

                 exactMatch = exactMatch, by = by)

           featureModules <- modules[featureIndex]

-          names(featureModules) <- features  

+          names(featureModules) <- features

         } else {

             stop("S4Vectors::metadata(altExp(sce, altExpName))$",

                 "celda_parameters$model must be",

@@ -60,5 +60,3 @@ setMethod("featureModuleLookup", signature(sce = "SingleCellExperiment"),

         return(featureModules)

     }

 )

-

-

@@ -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,

@@ -882,8 +882,8 @@ setMethod("plotRPC",

         diffMeansByK$L <- as.factor(diffMeansByK$L)

         diffMeansByK$rollmean <- data.table::frollmean(

             diffMeansByK$meanperpdiffK, n = n, align = "center")

-        diffMeansByK <- diffMeansByK[stats::complete.cases(diffMeansByK),]

-        

+        diffMeansByK <- diffMeansByK[stats::complete.cases(diffMeansByK), ]

+

         if (nlevels(dt$L) > 1) {

             plot <- ggplot2::ggplot(dt[!is.na(perpdiffK), ],

                 ggplot2::aes_string(x = "K",

@@ -939,8 +939,8 @@ setMethod("plotRPC",

         diffMeansByL$L <- as.factor(diffMeansByL$L)

         diffMeansByL$rollmean <- data.table::frollmean(

             diffMeansByL$meanperpdiffL, n = n, align = "center")

-        diffMeansByL <- diffMeansByL[stats::complete.cases(diffMeansByL),]

-        

+        diffMeansByL <- diffMeansByL[stats::complete.cases(diffMeansByL), ]

+

         plot <- ggplot2::ggplot(dt[!is.na(perpdiffL), ],

             ggplot2::aes_string(x = "L", y = "perpdiffL")) +

             ggplot2::geom_jitter(height = 0, width = 0.1,

@@ -1002,8 +1002,8 @@ setMethod("plotRPC",

         diffMeansByK$K <- as.factor(diffMeansByK$K)

         diffMeansByK$rollmean <- data.table::frollmean(

             diffMeansByK$meanperpdiffK, n = n, align = "center")

-        diffMeansByK <- diffMeansByK[stats::complete.cases(diffMeansByK),]

-        

+        diffMeansByK <- diffMeansByK[stats::complete.cases(diffMeansByK), ]

+

         plot <- ggplot2::ggplot(dt[!is.na(perpdiffK), ],

             ggplot2::aes_string(x = "K",

                 y = "perpdiffK")) +

@@ -1062,8 +1062,8 @@ setMethod("plotRPC",

         diffMeansByL$L <- as.factor(diffMeansByL$L)

         diffMeansByL$rollmean <- data.table::frollmean(

             diffMeansByL$meanperpdiffL, n = n, align = "center")

-        diffMeansByL <- diffMeansByL[stats::complete.cases(diffMeansByL),]

-        

+        diffMeansByL <- diffMeansByL[stats::complete.cases(diffMeansByL), ]

+

         plot <- ggplot2::ggplot(dt[!is.na(perpdiffL), ],

             ggplot2::aes_string(x = "L",

                 y = "perpdiffL")) +

@@ -47,25 +47,26 @@

 #' @return The plot as a ggplot object

 #' @export

 setGeneric("plotDimReduceGrid",

-    function(x,

-        reducedDimName,

-        dim1 = NULL,

-        dim2 = NULL,

-        useAssay = "counts",

-        altExpName = "featureSubset",

-        size = 1,

-        xlab = "Dimension_1",

-        ylab = "Dimension_2",

-        limits = c(-2, 2),

-        colorLow = "blue4",

-        colorMid = "grey90",

-        colorHigh = "firebrick1",

-        midpoint = 0,

-        varLabel = NULL,

-        ncol = NULL,

-        headers = NULL,

-        decreasing = FALSE) {

-    standardGeneric("plotDimReduceGrid")})

+           function(x,

+                    reducedDimName,

+                    dim1 = NULL,

+                    dim2 = NULL,

+                    useAssay = "counts",

+                    altExpName = "featureSubset",

+                    size = 1,

+                    xlab = "Dimension_1",

+                    ylab = "Dimension_2",

+                    limits = c(-2, 2),

+                    colorLow = "blue4",

+                    colorMid = "grey90",

+                    colorHigh = "firebrick1",

+                    midpoint = 0,

+                    varLabel = NULL,

+                    ncol = NULL,

+                    headers = NULL,

+                    decreasing = FALSE) {

+             standardGeneric("plotDimReduceGrid")

+           })

 #' @rdname plotDimReduceGrid

@@ -79,57 +80,57 @@ setGeneric("plotDimReduceGrid",

 #'   varLabel = "tSNE")

 #' @export

 setMethod("plotDimReduceGrid",

-    signature(x = "SingleCellExperiment"),

-    function(x,

-        reducedDimName,

-        dim1 = NULL,

-        dim2 = NULL,

-        useAssay = "counts",

-        altExpName = "featureSubset",

-        size = 1,

-        xlab = "Dimension_1",

-        ylab = "Dimension_2",

-        limits = c(-2, 2),

-        colorLow = "blue4",

-        colorMid = "grey90",

-        colorHigh = "firebrick1",

-        midpoint = 0,

-        varLabel = NULL,

-        ncol = NULL,

-        headers = NULL,

-        decreasing = FALSE) {

-

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

-        matrix <- SummarizedExperiment::assay(x, i = useAssay)

-

-        if (is.null(dim1)) {

-            dim1 <- SingleCellExperiment::reducedDim(altExp,

-                reducedDimName)[, 1]

-        }

-

-        if (is.null(dim2)) {

-            dim2 <- SingleCellExperiment::reducedDim(altExp,

-                reducedDimName)[, 2]

-        }

-

-        g <- .plotDimReduceGrid(dim1 = dim1,

-            dim2 = dim2,

-            matrix = matrix,

-            size = size,

-            xlab = xlab,

-            ylab = ylab,

-            limits = limits,

-            colorLow = colorLow,

-            colorMid = colorMid,

-            colorHigh = colorHigh,

-            midpoint = midpoint,

-            varLabel = varLabel,

-            ncol = ncol,

-            headers = headers,

-            decreasing = decreasing)

-        return(g)

-    }

-)

+          signature(x = "SingleCellExperiment"),

+          function(x,

+                   reducedDimName,

+                   dim1 = NULL,

+                   dim2 = NULL,

+                   useAssay = "counts",

+                   altExpName = "featureSubset",

+                   size = 1,

+                   xlab = "Dimension_1",

+                   ylab = "Dimension_2",

+                   limits = c(-2, 2),

+                   colorLow = "blue4",

+                   colorMid = "grey90",

+                   colorHigh = "firebrick1",

+                   midpoint = 0,

+                   varLabel = NULL,

+                   ncol = NULL,

+                   headers = NULL,

+                   decreasing = FALSE) {

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

+            matrix <- SummarizedExperiment::assay(x, i = useAssay)

+

+            if (is.null(dim1)) {

+              dim1 <- SingleCellExperiment::reducedDim(altExp,

+                                                       reducedDimName)[, 1]

+            }

+

+            if (is.null(dim2)) {

+              dim2 <- SingleCellExperiment::reducedDim(altExp,

+                                                       reducedDimName)[, 2]

+            }

+

+            g <- .plotDimReduceGrid(

+              dim1 = dim1,

+              dim2 = dim2,

+              matrix = matrix,

+              size = size,

+              xlab = xlab,

+              ylab = ylab,

+              limits = limits,

+              colorLow = colorLow,

+              colorMid = colorMid,

+              colorHigh = colorHigh,

+              midpoint = midpoint,

+              varLabel = varLabel,

+              ncol = ncol,

+              headers = headers,

+              decreasing = decreasing

+            )

+            return(g)

+          })

 #' @rdname plotDimReduceGrid

@@ -145,151 +146,142 @@ setMethod("plotDimReduceGrid",

 #'   varLabel = "tSNE")

 #' @export

 setMethod("plotDimReduceGrid",

-    signature(x = "ANY"),

-    function(x,

-        dim1,

-        dim2,

-        size = 1,

-        xlab = "Dimension_1",

-        ylab = "Dimension_2",

-        limits = c(-2, 2),

-        colorLow = "blue4",

-        colorMid = "grey90",

-        colorHigh = "firebrick1",

-        midpoint = 0,

-        varLabel = NULL,

-        ncol = NULL,

-        headers = NULL,

-        decreasing = FALSE) {

-

-        x <- as.matrix(x)

-        g <- .plotDimReduceGrid(dim1 = dim1,

-            dim2 = dim2,

-            matrix = x,

-            size = size,

-            xlab = xlab,

-            ylab = ylab,

-            limits = limits,

-            colorLow = colorLow,

-            colorMid = colorMid,

-            colorHigh = colorHigh,

-            midpoint = midpoint,

-            varLabel = varLabel,

-            ncol = ncol,

-            headers = headers,

-            decreasing = decreasing)

-        return(g)

-    }

-)

+          signature(x = "ANY"),

+          function(x,

+                   dim1,

+                   dim2,

+                   size = 1,

+                   xlab = "Dimension_1",

+                   ylab = "Dimension_2",

+                   limits = c(-2, 2),

+                   colorLow = "blue4",

+                   colorMid = "grey90",

+                   colorHigh = "firebrick1",

+                   midpoint = 0,

+                   varLabel = NULL,

+                   ncol = NULL,

+                   headers = NULL,

+                   decreasing = FALSE) {

+            x <- as.matrix(x)

+            g <- .plotDimReduceGrid(

+              dim1 = dim1,

+              dim2 = dim2,

+              matrix = x,

+              size = size,

+              xlab = xlab,

+              ylab = ylab,

+              limits = limits,

+              colorLow = colorLow,

+              colorMid = colorMid,

+              colorHigh = colorHigh,

+              midpoint = midpoint,

+              varLabel = varLabel,

+              ncol = ncol,

+              headers = headers,

+              decreasing = decreasing

+            )

+            return(g)

+          })

 #' @importFrom reshape2 melt

 .plotDimReduceGrid <- function(dim1,

-    dim2,

-    matrix,

-    size,

-    xlab,

-    ylab,

-    limits,

-    colorLow,

-    colorMid,

-    colorHigh,

-    midpoint,

-    varLabel,

-    ncol,

-    headers,

-    decreasing) {

-

-    df <- data.frame(dim1, dim2, t(as.data.frame(matrix)), check.names = FALSE)

-    naIx <- is.na(dim1) | is.na(dim2)

-    df <- df[!naIx, ]

-

-    m <- reshape2::melt(df, id.vars = c("dim1", "dim2"))

-    colnames(m) <- c(xlab, ylab, "facet", "Expression")

-

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

-        m <- m[order(m$facet, m$Expression, decreasing = decreasing), ]

-    }

+                               dim2,

+                               matrix,

+                               size,

+                               xlab,

+                               ylab,

+                               limits,

+                               colorLow,

+                               colorMid,

+                               colorHigh,

+                               midpoint,

+                               varLabel,

+                               ncol,

+                               headers,

+                               decreasing) {

+  df <-

+    data.frame(dim1, dim2, t(as.data.frame(matrix)), check.names = FALSE)

+  naIx <- is.na(dim1) | is.na(dim2)

+  df <- df[!naIx, ]

-    if (is.null(midpoint)) {

-        midpoint <- mean(m[, 4], trim = 0.1)

-    }

+  m <- reshape2::melt(df, id.vars = c("dim1", "dim2"))

+  colnames(m) <- c(xlab, ylab, "facet", "Expression")

-    varLabel <- gsub("_", " ", varLabel)

-

-    if (isFALSE(is.null(headers))) {

-        names(headers) <- levels(m$facet)

-        headers <- ggplot2::as_labeller(headers)

-

-        g <- ggplot2::ggplot(

-            m,

-            ggplot2::aes_string(x = xlab, y = ylab)

-        ) +

-            ggplot2::geom_point(

-                stat = "identity",

-                size = size,

-                ggplot2::aes_string(color = m$Expression)

-            ) +

-            ggplot2::theme_bw() +

-            ggplot2::scale_colour_gradient2(

-                limits = limits,

-                low = colorLow,

-                high = colorHigh,

-                mid = colorMid,

-                midpoint = midpoint,

-                name = varLabel

-            ) +

-            ggplot2::theme(

-                strip.background = ggplot2::element_blank(),

-                panel.grid.major = ggplot2::element_blank(),

-                panel.grid.minor = ggplot2::element_blank(),

-                panel.spacing = unit(0, "lines"),

-                panel.background = ggplot2::element_blank(),

-                axis.line = ggplot2::element_line(colour = "black")

-            )

-        if (isFALSE(is.null(ncol))) {

-            g <- g + ggplot2::facet_wrap(~facet,

-                labeller = headers,

-                ncol = ncol

-            )

-        } else {

-            g <- g + ggplot2::facet_wrap(~facet, labeller = headers)

-        }

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

+    m <- m[order(m$facet, m$Expression, decreasing = decreasing), ]

+  }

+

+  if (is.null(midpoint)) {

+    midpoint <- mean(m[, 4], trim = 0.1)

+  }

+

+  varLabel <- gsub("_", " ", varLabel)

+

+  if (isFALSE(is.null(headers))) {

+    names(headers) <- levels(m$facet)

+    headers <- ggplot2::as_labeller(headers)

+

+    g <- ggplot2::ggplot(m,

+                         ggplot2::aes_string(x = xlab, y = ylab)) +

+      ggplot2::geom_point(stat = "identity",

+                          size = size,

+                          ggplot2::aes_string(color = m$Expression)) +

+      ggplot2::theme_bw() +

+      ggplot2::scale_colour_gradient2(

+        limits = limits,

+        low = colorLow,

+        high = colorHigh,

+        mid = colorMid,

+        midpoint = midpoint,

+        name = varLabel

+      ) +

+      ggplot2::theme(

+        strip.background = ggplot2::element_blank(),

+        panel.grid.major = ggplot2::element_blank(),

+        panel.grid.minor = ggplot2::element_blank(),

+        panel.spacing = unit(0, "lines"),

+        panel.background = ggplot2::element_blank(),

+        axis.line = ggplot2::element_line(colour = "black")

+      )

+    if (isFALSE(is.null(ncol))) {

+      g <- g + ggplot2::facet_wrap(~ facet,

+                                  labeller = headers,

+                                  ncol = ncol)

     } else {

-        g <- ggplot2::ggplot(

-            m,

-            ggplot2::aes_string(x = xlab, y = ylab)

-        ) +

-            ggplot2::geom_point(

-                stat = "identity",

-                size = size,

-                ggplot2::aes_string(color = m$Expression)

-            ) +

-            ggplot2::facet_wrap(~facet) +

-            ggplot2::theme_bw() +

-            ggplot2::scale_colour_gradient2(

-                limits = limits,

-                low = colorLow,

-                high = colorHigh,

-                mid = colorMid,

-                midpoint = midpoint,

-                name = varLabel

-            ) +

-            ggplot2::theme(

-                strip.background = ggplot2::element_blank(),

-                panel.grid.major = ggplot2::element_blank(),

-                panel.grid.minor = ggplot2::element_blank(),

-                panel.spacing = unit(0, "lines"),

-                panel.background = ggplot2::element_blank(),

-                axis.line = ggplot2::element_line(colour = "black")

-            )

-        if (isFALSE(is.null(ncol))) {

-            g <- g + ggplot2::facet_wrap(~facet, ncol = ncol)

-        } else {

-            g <- g + ggplot2::facet_wrap(~facet)

-        }

+      g <- g + ggplot2::facet_wrap(~ facet, labeller = headers)

     }

-    return(g)

+  } else {

+    g <- ggplot2::ggplot(m,

+                         ggplot2::aes_string(x = xlab, y = ylab)) +

+      ggplot2::geom_point(stat = "identity",

+                          size = size,

+                          ggplot2::aes_string(color = m$Expression)) +

+      ggplot2::facet_wrap(~ facet) +

+      ggplot2::theme_bw() +

+      ggplot2::scale_colour_gradient2(

+        limits = limits,

+        low = colorLow,

+        high = colorHigh,

+        mid = colorMid,

+        midpoint = midpoint,

+        name = varLabel

+      ) +

+      ggplot2::theme(

+        strip.background = ggplot2::element_blank(),

+        panel.grid.major = ggplot2::element_blank(),

+        panel.grid.minor = ggplot2::element_blank(),

+        panel.spacing = unit(0, "lines"),

+        panel.background = ggplot2::element_blank(),

+        axis.line = ggplot2::element_line(colour = "black")

+      )

+    if (isFALSE(is.null(ncol))) {

+      g <- g + ggplot2::facet_wrap(~ facet, ncol = ncol)

+    } else {

+      g <- g + ggplot2::facet_wrap(~ facet)

+    }

+  }

+  return(g)

 }

@@ -366,30 +358,30 @@ setMethod("plotDimReduceGrid",

 #' @return The plot as a ggplot object

 #' @export

 setGeneric("plotDimReduceFeature", function(x,

-    features,

-    reducedDimName = NULL,

-    displayName = NULL,    

-    dim1 = NULL,

-    dim2 = NULL,

-    headers = NULL,

-    useAssay = "counts",

-    altExpName = "featureSubset",

-    normalize = FALSE,

-    zscore = TRUE,

-    exactMatch = TRUE,

-    trim = c(-2, 2),

-    limits = c(-2, 2),

-    size = 0.5,

-    xlab = NULL,

-    ylab = NULL,

-    colorLow = "blue4",

-    colorMid = "grey90",

-    colorHigh = "firebrick1",

-    midpoint = 0,

-    ncol = NULL,

-    decreasing = FALSE) {

-

-    standardGeneric("plotDimReduceFeature")})

+                                            features,

+                                            reducedDimName = NULL,

+                                            displayName = NULL,

+                                            dim1 = NULL,

+                                            dim2 = NULL,

+                                            headers = NULL,

+                                            useAssay = "counts",

+                                            altExpName = "featureSubset",

+                                            normalize = FALSE,

+                                            zscore = TRUE,

+                                            exactMatch = TRUE,

+                                            trim = c(-2, 2),

+                                            limits = c(-2, 2),

+                                            size = 0.5,

+                                            xlab = NULL,

+                                            ylab = NULL,

+                                            colorLow = "blue4",

+                                            colorMid = "grey90",

+                                            colorHigh = "firebrick1",

+                                            midpoint = 0,

+                                            ncol = NULL,

+                                            decreasing = FALSE) {

+  standardGeneric("plotDimReduceFeature")

+})

 #' @rdname plotDimReduceFeature

@@ -403,92 +395,91 @@ setGeneric("plotDimReduceFeature", function(x,

 #'   exactMatch = TRUE)

 #' @export

 setMethod("plotDimReduceFeature",

-    signature(x = "SingleCellExperiment"),

-    function(x,

-        features,

-        reducedDimName,

-        displayName = NULL,

-        dim1 = 1,

-        dim2 = 2,

-        headers = NULL,

-        useAssay = "counts",

-        altExpName = "featureSubset",

-        normalize = FALSE,

-        zscore = TRUE,

-        exactMatch = TRUE,

-        trim = c(-2, 2),

-        limits = c(-2, 2),

-        size = 0.5,

-        xlab = NULL,

-        ylab = NULL,

-        colorLow = "blue4",

-        colorMid = "grey90",

-        colorHigh = "firebrick1",

-        midpoint = 0,

-        ncol = NULL,

-        decreasing = FALSE) {

-

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

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

-        reddim <- .processReducedDim(x = altExp,

-                                     reducedDimName = reducedDimName,

-                                     dim1 = dim1,

-                                     dim2 = dim2,

-                                     xlab = xlab,

-                                     ylab = ylab)

-        

-        if (isFALSE(is.null(displayName))) {

-            featuresIx <- retrieveFeatureIndex(features,

-                x,

-                by = displayName,

-                exactMatch = exactMatch)

-            headers <- SummarizedExperiment::rowData(x)[[

-                displayName]][featuresIx]

-        } else {

-            featuresIx <- retrieveFeatureIndex(features,

-                counts,

-                by = "rownames",

-                exactMatch = exactMatch)

+          signature(x = "SingleCellExperiment"),

+          function(x,

+                   features,

+                   reducedDimName,

+                   displayName = NULL,

+                   dim1 = 1,

+                   dim2 = 2,

+                   headers = NULL,

+                   useAssay = "counts",

+                   altExpName = "featureSubset",

+                   normalize = FALSE,

+                   zscore = TRUE,

+                   exactMatch = TRUE,

+                   trim = c(-2, 2),

+                   limits = c(-2, 2),

+                   size = 0.5,

+                   xlab = NULL,

+                   ylab = NULL,

+                   colorLow = "blue4",

+                   colorMid = "grey90",

+                   colorHigh = "firebrick1",

+                   midpoint = 0,

+                   ncol = NULL,

+                   decreasing = FALSE) {

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

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

+            reddim <- .processReducedDim(

+              x = altExp,

+              reducedDimName = reducedDimName,

+              dim1 = dim1,

+              dim2 = dim2,

+              xlab = xlab,

+              ylab = ylab

+            )

-            if (isFALSE(is.null(headers))) {

+            if (isFALSE(is.null(displayName))) {

+              featuresIx <- retrieveFeatureIndex(features,

+                                                 x,

+                                                 by = displayName,

+                                                 exactMatch = exactMatch)

+        headers <- SummarizedExperiment::rowData(x)[[displayName]][featuresIx]

+            } else {

+              featuresIx <- retrieveFeatureIndex(features,

+                                                 counts,

+                                                 by = "rownames",

+                                                 exactMatch = exactMatch)

+

+              if (isFALSE(is.null(headers))) {

                 if (length(headers) != length(features)) {

-                    stop(

-                        "Headers ",

-                        headers,

-                        " should be the same length as features ",

-                        features

-                    )

+                  stop("Headers ",

+                       headers,

+                       " should be the same length as features ",

+                       features)

                 }

                 if (isFALSE(exactMatch)) {

-                    warning("exactMatch is FALSE. headers will not be used!")

-                    headers <- NULL

+                  warning("exactMatch is FALSE. headers will not be used!")

+                  headers <- NULL

                 }

+              }

             }

-        }

-

-        g <- .plotDimReduceFeature(dim1 = reddim$dim1,

-            dim2 = reddim$dim2,

-            counts = counts,

-            features = features,

-            headers = headers,

-            normalize = normalize,

-            zscore = zscore,

-            featuresIx = featuresIx,

-            trim = trim,

-            limits = limits,

-            size = size,

-            xlab = reddim$xlab,

-            ylab = reddim$ylab,

-            colorLow = colorLow,

-            colorMid = colorMid,

-            colorHigh = colorHigh,

-            midpoint = midpoint,

-            ncol = ncol,

-            decreasing = decreasing)

-        return(g)

-    }

-)

+

+            g <- .plotDimReduceFeature(

+              dim1 = reddim$dim1,

+              dim2 = reddim$dim2,

+              counts = counts,

+              features = features,

+              headers = headers,

+              normalize = normalize,

+              zscore = zscore,

+              featuresIx = featuresIx,

+              trim = trim,

+              limits = limits,

+              size = size,

+              xlab = reddim$xlab,

+              ylab = reddim$ylab,

+              colorLow = colorLow,

+              colorMid = colorMid,

+              colorHigh = colorHigh,

+              midpoint = midpoint,

+              ncol = ncol,

+              decreasing = decreasing

+            )

+            return(g)

+          })

 #' @rdname plotDimReduceFeature

@@ -504,93 +495,90 @@ setMethod("plotDimReduceFeature",

 #'   exactMatch = TRUE)

 #' @export

 setMethod("plotDimReduceFeature",

-    signature(x = "ANY"),

-    function(x,

-        features,

-        dim1,

-        dim2,

-        headers = NULL,

-        normalize = FALSE,

-        zscore = TRUE,

-        exactMatch = TRUE,

-        trim = c(-2, 2),

-        limits = c(-2, 2),

-        size = 0.5,

-        xlab = "Dimension_1",

-        ylab = "Dimension_2",

-        colorLow = "blue4",

-        colorMid = "grey90",

-        colorHigh = "firebrick1",

-        midpoint = 0,

-        ncol = NULL,

-        decreasing = FALSE) {

-

-        x <- as.matrix(x)

-        if (isFALSE(is.null(headers))) {

-            if (length(headers) != length(features)) {

-                stop(

-                    "Headers ",

-                    headers,

-                    " should be the same length as features ",

-                    features

-                )

-            }

-

-            if (isFALSE(exactMatch)) {

+          signature(x = "ANY"),

+          function(x,

+                   features,

+                   dim1,

+                   dim2,

+                   headers = NULL,

+                   normalize = FALSE,

+                   zscore = TRUE,

+                   exactMatch = TRUE,

+                   trim = c(-2, 2),

+                   limits = c(-2, 2),

+                   size = 0.5,

+                   xlab = "Dimension_1",

+                   ylab = "Dimension_2",

+                   colorLow = "blue4",

+                   colorMid = "grey90",

+                   colorHigh = "firebrick1",

+                   midpoint = 0,

+                   ncol = NULL,

+                   decreasing = FALSE) {

+            x <- as.matrix(x)

+            if (isFALSE(is.null(headers))) {

+              if (length(headers) != length(features)) {

+                stop("Headers ",

+                     headers,

+                     " should be the same length as features ",

+                     features)

+              }

+

+              if (isFALSE(exactMatch)) {

                 warning("exactMatch is FALSE. headers will not be used!")

                 headers <- NULL

+              }

             }