@@ -882,7 +882,7 @@ setMethod("plotRPC",

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

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

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

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

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

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

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

@@ -939,7 +939,7 @@ setMethod("plotRPC",

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

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

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

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

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

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

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

@@ -1002,7 +1002,7 @@ setMethod("plotRPC",

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

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

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

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

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

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

             ggplot2::aes_string(x = "K",

@@ -1062,7 +1062,7 @@ setMethod("plotRPC",

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

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

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

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

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

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

             ggplot2::aes_string(x = "L",

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

 #'  \code{reducedDimNames(x)} if \code{x} is a

 #'  \linkS4class{SingleCellExperiment} object. Ignored if both \code{dim1} and

 #'  \code{dim2} are set.

-#' @param dim1 Numeric vector. First dimension from data dimension

+#' @param dim1 Numeric vector. Second dimension from data dimension

 #'  reduction output.

 #' @param dim2 Numeric vector. Second dimension from data dimension

 #'  reduction output.

@@ -302,19 +302,23 @@ setMethod("plotDimReduceGrid",

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

 #'  represent features and columns represent cells.

 #' @param features Character vector. Features in the rownames of counts to plot.

+#' @param reducedDimName The name of the dimension reduction slot in

+#'  \code{reducedDimNames(x)} if \code{x} is a

+#'  \linkS4class{SingleCellExperiment} object. If \code{NULL}, then both

+#'  \code{dim1} and \code{dim2} need to be set. Default \code{NULL}.

 #' @param displayName Character. The column name of

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

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

 #'  if \code{x} is a \linkS4class{SingleCellExperiment} object. Overwrites

 #'  \code{headers}.

-#' @param reducedDimName The name of the dimension reduction slot in

-#'  \code{reducedDimNames(x)} if \code{x} is a

-#'  \linkS4class{SingleCellExperiment} object. If \code{NULL}, then both

-#'  \code{dim1} and \code{dim2} need to be set. Default \code{NULL}.

-#' @param dim1 Numeric vector. First dimension from data

-#'  dimension reduction output to be plotted on the x-axis. Default \code{NULL}.

-#' @param dim2 Numeric vector. Second dimension from data dimension

-#'  reduction output to be plotted on the y-axis. Default \code{NULL}.

+#' @param dim1 Integer or numeric vector. If \code{reducedDimName} is supplied,

+#'  then, this will be used as an index to determine which dimension will be

+#'  plotted on the x-axis. If \code{reducedDimName} is not supplied, then this

+#'  should be a vector which will be plotted on the x-axis. Default \code{1}.

+#' @param dim2 Integer or numeric vector. If \code{reducedDimName} is supplied,

+#'  then, this will be used as an index to determine which dimension will be

+#'  plotted on the y-axis. If \code{reducedDimName} is not supplied, then this

+#'  should be a vector which will be plotted on the y-axis. Default \code{2}.

 #' @param headers Character vector. If \code{NULL}, the corresponding

 #'  rownames are used as labels. Otherwise, these headers are used to label

 #'  the features. Only works if \code{displayName} is \code{NULL} and

@@ -363,8 +367,8 @@ setMethod("plotDimReduceGrid",

 #' @export

 setGeneric("plotDimReduceFeature", function(x,

     features,

-    displayName = NULL,

     reducedDimName = NULL,

+    displayName = NULL,    

     dim1 = NULL,

     dim2 = NULL,

     headers = NULL,

@@ -375,9 +379,9 @@ setGeneric("plotDimReduceFeature", function(x,

     exactMatch = TRUE,

     trim = c(-2, 2),

     limits = c(-2, 2),

-    size = 1,

-    xlab = "Dimension_1",

-    ylab = "Dimension_2",

+    size = 0.5,

+    xlab = NULL,

+    ylab = NULL,

     colorLow = "blue4",

     colorMid = "grey90",

     colorHigh = "firebrick1",

@@ -402,10 +406,10 @@ setMethod("plotDimReduceFeature",

     signature(x = "SingleCellExperiment"),

     function(x,

         features,

+        reducedDimName,

         displayName = NULL,

-        reducedDimName = NULL,

-        dim1 = NULL,

-        dim2 = NULL,

+        dim1 = 1,

+        dim2 = 2,

         headers = NULL,

         useAssay = "counts",

         altExpName = "featureSubset",

@@ -414,9 +418,9 @@ setMethod("plotDimReduceFeature",

         exactMatch = TRUE,

         trim = c(-2, 2),

         limits = c(-2, 2),

-        size = 1,

-        xlab = "Dimension_1",

-        ylab = "Dimension_2",

+        size = 0.5,

+        xlab = NULL,

+        ylab = NULL,

         colorLow = "blue4",

         colorMid = "grey90",

         colorHigh = "firebrick1",

@@ -426,21 +430,13 @@ setMethod("plotDimReduceFeature",

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

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

-

-        if (is.null(reducedDimName)) {

-          if (is.null(dim1) | is.null(dim2)) {

-            stop("If 'reducedDimName' is not supplied, then 'dim1' and 'dim2' ",

-                 "must be specified.")

-          }

-          if (length(dim1) != length(dim2)) {

-            stop("'dim1' and 'dim2' must be the same length.")

-          }

-        } else{

-          dims <- SingleCellExperiment::reducedDim(altExp, reducedDimName)

-          dim1 <- dims[, 1]

-          dim2 <- dims[, 2]

-        }

-

+        reddim <- .processReducedDim(x = altExp,

+                                     reducedDimName = reducedDimName,

+                                     dim1 = dim1,

+                                     dim2 = dim2,

+                                     xlab = xlab,

+                                     ylab = ylab)

+        

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

             featuresIx <- retrieveFeatureIndex(features,

                 x,

@@ -471,8 +467,8 @@ setMethod("plotDimReduceFeature",

             }

         }

-        g <- .plotDimReduceFeature(dim1 = dim1,

-            dim2 = dim2,

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

+            dim2 = reddim$dim2,

             counts = counts,

             features = features,

             headers = headers,

@@ -482,8 +478,8 @@ setMethod("plotDimReduceFeature",

             trim = trim,

             limits = limits,

             size = size,

-            xlab = xlab,

-            ylab = ylab,

+            xlab = reddim$xlab,

+            ylab = reddim$ylab,

             colorLow = colorLow,

             colorMid = colorMid,

             colorHigh = colorHigh,

@@ -519,7 +515,7 @@ setMethod("plotDimReduceFeature",

         exactMatch = TRUE,

         trim = c(-2, 2),

         limits = c(-2, 2),

-        size = 1,

+        size = 0.5,

         xlab = "Dimension_1",

         ylab = "Dimension_2",

         colorLow = "blue4",

@@ -660,10 +656,14 @@ setMethod("plotDimReduceFeature",

 #'  \code{reducedDimNames(x)} if \code{x} is a

 #'  \linkS4class{SingleCellExperiment} object. Ignored if both \code{dim1} and

 #'  \code{dim2} are set.

-#' @param dim1 Numeric vector.

-#'  First dimension from data dimension reduction output.

-#' @param dim2 Numeric vector.

-#'  Second dimension from data dimension reduction output.

+#' @param dim1 Integer or numeric vector. If \code{reducedDimName} is supplied,

+#'  then, this will be used as an index to determine which dimension will be

+#'  plotted on the x-axis. If \code{reducedDimName} is not supplied, then this

+#'  should be a vector which will be plotted on the x-axis. Default \code{1}.

+#' @param dim2 Integer or numeric vector. If \code{reducedDimName} is supplied,

+#'  then, this will be used as an index to determine which dimension will be

+#'  plotted on the y-axis. If \code{reducedDimName} is not supplied, then this

+#'  should be a vector which will be plotted on the y-axis. Default \code{2}.

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

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

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

@@ -673,15 +673,15 @@ setMethod("plotDimReduceFeature",

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

 #' @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 limits Passed to \link{scale_colour_gradient}. The range

-#'  of color scale.

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

+#' @param size Numeric. Sets size of point on plot. Default 0.5.

 #' @param xlab Character vector. Label for the x-axis. Default "Dimension_1".

 #' @param ylab Character vector. Label for the y-axis. Default "Dimension_2".

 #' @param colorLow Character. A color available from `colors()`.

 #'  The color will be used to signify the lowest values on the scale.

+#' @param rescale Logical.

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

+#' @param limits Passed to \link{scale_colour_gradient}. The range

+#'  of color scale.

 #' @param colorHigh Character. A color available from `colors()`.

 #'  The color will be used to signify the highest values on the scale.

 #' @param ncol Integer. Passed to \link[ggplot2]{facet_wrap}. Specify the

@@ -696,17 +696,17 @@ setMethod("plotDimReduceFeature",

 setGeneric("plotDimReduceModule",

     function(x,

         reducedDimName,

-        dim1 = NULL,

-        dim2 = NULL,

         useAssay = "counts",

         altExpName = "featureSubset",

         celdaMod,

         modules = NULL,

+        dim1 = NULL,

+        dim2 = NULL,

+        size = 0.5,

+        xlab = NULL,

+        ylab = NULL,

         rescale = TRUE,

         limits = c(0, 1),

-        size = 1,

-        xlab = "Dimension_1",

-        ylab = "Dimension_2",

         colorLow = "grey90",

         colorHigh = "firebrick1",

         ncol = NULL,

@@ -726,49 +726,44 @@ setMethod("plotDimReduceModule",

     signature(x = "SingleCellExperiment"),

     function(x,

         reducedDimName,

-        dim1 = NULL,

-        dim2 = NULL,

         useAssay = "counts",

         altExpName = "featureSubset",

         modules = NULL,

+        dim1 = 1,

+        dim2 = 2,

+        size = 0.5,

+        xlab = NULL,

+        ylab = NULL,

         rescale = TRUE,

         limits = c(0, 1),

-        size = 1,

-        xlab = "Dimension_1",

-        ylab = "Dimension_2",

         colorLow = "grey90",

         colorHigh = "firebrick1",

         ncol = NULL,

         decreasing = FALSE) {

+        # Get reduced dim object

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

+        reddim <- .processReducedDim(x = altExp,

+                                     reducedDimName = reducedDimName,

+                                     dim1 = dim1,

+                                     dim2 = dim2,

+                                     xlab = xlab,

+                                     ylab = ylab)

-        if (is.null(dim1)) {

-            dim1 <- SingleCellExperiment::reducedDim(altExp,

-                reducedDimName)[, 1]

-        }

-

-        if (is.null(dim2)) {

-            dim2 <- SingleCellExperiment::reducedDim(altExp,

-                reducedDimName)[, 2]

-        }

-

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

         factorized <- factorizeMatrix(x,

             useAssay = useAssay,

             altExpName = altExpName,

             type = "proportion")

-        g <- .plotDimReduceModule(dim1 = dim1,

-            dim2 = dim2,

-            counts = counts,

+        g <- .plotDimReduceModule(dim1 = reddim$dim1,

+            dim2 = reddim$dim2,

             factorized = factorized,

             modules = modules,

             rescale = rescale,

             limits = limits,

             size = size,

-            xlab = xlab,

-            ylab = ylab,

+            xlab = reddim$xlab,

+            ylab = reddim$ylab,

             colorLow = colorLow,

             colorHigh = colorHigh,

             ncol = ncol,

@@ -792,32 +787,36 @@ setMethod("plotDimReduceModule",

 setMethod("plotDimReduceModule",

     signature(x = "ANY"),

     function(x,

-        dim1,

-        dim2,

         celdaMod,

         modules = NULL,

-        rescale = TRUE,

-        limits = c(0, 1),

-        size = 1,

+        dim1,

+        dim2,

+        size = 0.5,

         xlab = "Dimension_1",

         ylab = "Dimension_2",

+        rescale = TRUE,

+        limits = c(0, 1),

         colorLow = "grey90",

         colorHigh = "firebrick1",

         ncol = NULL,

         decreasing = FALSE) {

-        x <- as.matrix(x)

         factorized <- factorizeMatrix(x = x, celdaMod = celdaMod)

-        g <- .plotDimReduceModule(dim1 = dim1,

-            dim2 = dim2,

-            counts = x,

+        reddim <- .processReducedDim(x = x,

+                                     dim1 = dim1,

+                                     dim2 = dim2,

+                                     xlab = xlab,

+                                     ylab = ylab)

+        

+        g <- .plotDimReduceModule(dim1 = reddim$dim1,

+            dim2 = reddim$dim2,

             factorized = factorized,

             modules = modules,

             rescale = rescale,

             limits = limits,

             size = size,

-            xlab = xlab,

-            ylab = ylab,

+            xlab = reddim$xlab,

+            ylab = reddim$ylab,

             colorLow = colorLow,

             colorHigh = colorHigh,

             ncol = ncol,

@@ -829,7 +828,6 @@ setMethod("plotDimReduceModule",

 .plotDimReduceModule <- function(dim1,

     dim2,

-    counts,

     factorized,

     modules,

     rescale,

@@ -921,13 +919,17 @@ setMethod("plotDimReduceModule",

 #'  \code{dim2} are set.

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

 #'  to use. Default "featureSubset".

-#' @param dim1 Numeric vector. First dimension from data

-#'  dimension reduction output.

-#' @param dim2 Numeric vector. Second dimension from data

-#'  dimension reduction output.

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

-#' @param xlab Character vector. Label for the x-axis. Default "Dimension_1".

-#' @param ylab Character vector. Label for the y-axis. Default "Dimension_2".

+#' @param dim1 Integer or numeric vector. If \code{reducedDimName} is supplied,

+#'  then, this will be used as an index to determine which dimension will be

+#'  plotted on the x-axis. If \code{reducedDimName} is not supplied, then this

+#'  should be a vector which will be plotted on the x-axis. Default \code{1}.

+#' @param dim2 Integer or numeric vector. If \code{reducedDimName} is supplied,

+#'  then, this will be used as an index to determine which dimension will be

+#'  plotted on the y-axis. If \code{reducedDimName} is not supplied, then this

+#'  should be a vector which will be plotted on the y-axis. Default \code{2}.

+#' @param size Numeric. Sets size of point on plot. Default \code{0.5}.

+#' @param xlab Character vector. Label for the x-axis. Default \code{NULL}.

+#' @param ylab Character vector. Label for the y-axis. Default \code{NULL}.

 #' @param specificClusters Numeric vector.

 #'  Only color cells in the specified clusters.

 #'  All other cells will be grey.

@@ -947,9 +949,9 @@ setGeneric("plotDimReduceCluster",

         altExpName = "featureSubset",

         dim1 = NULL,

         dim2 = NULL,

-        size = 1,

-        xlab = "Dimension_1",

-        ylab = "Dimension_2",

+        size = 0.5,

+        xlab = NULL,

+        ylab = NULL,

         specificClusters = NULL,

         labelClusters = FALSE,

         groupBy = NULL,

@@ -970,11 +972,11 @@ setMethod("plotDimReduceCluster",

     function(x,

         reducedDimName,

         altExpName = "featureSubset",

-        dim1 = NULL,

-        dim2 = NULL,

-        size = 1,

-        xlab = "Dimension_1",

-        ylab = "Dimension_2",

+        dim1 = 1,

+        dim2 = 2,

+        size = 0.5,

+        xlab = NULL,

+        ylab = NULL,

         specificClusters = NULL,

         labelClusters = FALSE,

         groupBy = NULL,

@@ -989,22 +991,19 @@ setMethod("plotDimReduceCluster",

         }

         cluster <- SummarizedExperiment::colData(altExp)[["celda_cell_cluster"]]

-        if (is.null(dim1)) {

-            dim1 <- SingleCellExperiment::reducedDim(altExp,

-                reducedDimName)[, 1]

-        }

-

-        if (is.null(dim2)) {

-            dim2 <- SingleCellExperiment::reducedDim(altExp,

-                reducedDimName)[, 2]

-        }

+        reddim <- .processReducedDim(x = altExp,

+                                     reducedDimName = reducedDimName,

+                                     dim1 = dim1,

+                                     dim2 = dim2,

+                                     xlab = xlab,

+                                     ylab = ylab)

-        g <- .plotDimReduceCluster(dim1 = dim1,

-            dim2 = dim2,

+        g <- .plotDimReduceCluster(dim1 = reddim$dim1,

+            dim2 = reddim$dim2,

             cluster = cluster,

             size = size,

-            xlab = xlab,

-            ylab = ylab,

+            xlab = reddim$xlab,

+            ylab = reddim$ylab,

             specificClusters = specificClusters,

             labelClusters = labelClusters,

             groupBy = groupBy,

@@ -1029,7 +1028,7 @@ setMethod("plotDimReduceCluster",

     function(x,

         dim1,

         dim2,

-        size = 1,

+        size = 0.5,

         xlab = "Dimension_1",

         ylab = "Dimension_2",

         specificClusters = NULL,

@@ -1037,12 +1036,17 @@ setMethod("plotDimReduceCluster",

         groupBy = NULL,

         labelSize = 3.5) {

-        g <- .plotDimReduceCluster(dim1 = dim1,

-            dim2 = dim2,

+      reddim <- .processReducedDim(x = x,

+                                   dim1 = dim1,

+                                   dim2 = dim2,

+                                   xlab = xlab,

+                                   ylab = ylab)

+      g <- .plotDimReduceCluster(dim1 = reddim$dim1,

+            dim2 = reddim$dim2,

             cluster = x,

             size = size,

-            xlab = xlab,

-            ylab = ylab,

+            xlab = reddim$xlab,

+            ylab = reddim$ylab,

             specificClusters = specificClusters,

             labelClusters = labelClusters,

             groupBy = groupBy,

@@ -1305,3 +1309,59 @@ setMethod("plotCeldaViolin",

     return(p)

 }

+

+

+

+

+.processReducedDim <- function(x,

+                           reducedDimName = NULL,

+                           dim1 = NULL,

+                           dim2 = NULL,

+                           xlab = NULL,

+                           ylab = NULL) {

+  if(inherits(x, "SingleCellExperiment") & !is.null(reducedDimName)) {

+    reddim <- SingleCellExperiment::reducedDim(x, reducedDimName)

+    

+    # Get dims to retrieve from redDim object

+    if(is.null(dim1)) dim1 <- 1

+    if(is.null(dim2)) dim2 <- 2

+    

+    # Get labels

+    xlab <- colnames(reddim)[dim1]

+    ylab <- colnames(reddim)[dim2]

+    

+    # Set up return object

+    res <- list(dim1 = reddim[,dim1], dim2 = reddim[,dim2], xlab = xlab, ylab = ylab)

+    

+  } else if (!is.null(dim1) & !is.null(dim2)) {

+    if(inherits(x, c("matrix", "Matrix"))) {

+      if(length(dim1) != ncol(x)) {

+        stop("'dim1' needs to be the same length as 'x'.")

+      }

+      if(length(dim2) != ncol(x)) {

+        stop("'dim2' needs to be the same length as 'x'.")

+      }

+    } else {

+      if(length(dim1) != length(x)) {

+        stop("'dim1' needs to be the same length as 'x'.")

+      }

+      if(length(dim2) != length(x)) {

+        stop("'dim2' needs to be the same length as 'x'.")

+      }

+    }

+    if(is.null(xlab)) xlab <- "Dimension 1"

+    if(is.null(ylab)) ylab <- "Dimension 2"

+    

+    res <- list(dim1 = dim1, dim2 = dim2, xlab = xlab, ylab = ylab)

+    

+  } else {

+    stop("'x' can be supplied as a SingleCelExperiment along with ",

+    "'reducedDimName' and 'dim1' and 'dim2' can be used to specify which ",

+    "dimensions to plot on the x- and y-axis, respectively. Alternatively, ",

+    "'x', 'dim1' and 'dim2' can be supplied as vectors of the same length ",

+    "where 'dim1' is the x-axis, 'dim2', is the y-axis, and 'x' will be used ",

+    "to color the points.")

+  }

+  

+  return(res)

+} 

@@ -12,9 +12,9 @@ plotDimReduceCluster(

   altExpName = "featureSubset",

   dim1 = NULL,

   dim2 = NULL,

-  size = 1,

-  xlab = "Dimension_1",

-  ylab = "Dimension_2",

+  size = 0.5,

+  xlab = NULL,

+  ylab = NULL,

   specificClusters = NULL,

   labelClusters = FALSE,

   groupBy = NULL,

@@ -25,11 +25,11 @@ plotDimReduceCluster(

   x,

   reducedDimName,

   altExpName = "featureSubset",

-  dim1 = NULL,

-  dim2 = NULL,

-  size = 1,

-  xlab = "Dimension_1",

-  ylab = "Dimension_2",

+  dim1 = 1,

+  dim2 = 2,

+  size = 0.5,

+  xlab = NULL,

+  ylab = NULL,

   specificClusters = NULL,

   labelClusters = FALSE,

   groupBy = NULL,

@@ -40,7 +40,7 @@ plotDimReduceCluster(

   x,

   dim1,

   dim2,

-  size = 1,

+  size = 0.5,

   xlab = "Dimension_1",

   ylab = "Dimension_2",

   specificClusters = NULL,

@@ -63,17 +63,21 @@ column in \code{colData(x)}.}

 \item{altExpName}{The name for the \link{altExp} slot

 to use. Default "featureSubset".}

-\item{dim1}{Numeric vector. First dimension from data

-dimension reduction output.}

+\item{dim1}{Integer or numeric vector. If \code{reducedDimName} is supplied,

+then, this will be used as an index to determine which dimension will be

+plotted on the x-axis. If \code{reducedDimName} is not supplied, then this

+should be a vector which will be plotted on the x-axis. Default \code{1}.}

-\item{dim2}{Numeric vector. Second dimension from data

-dimension reduction output.}

+\item{dim2}{Integer or numeric vector. If \code{reducedDimName} is supplied,

+then, this will be used as an index to determine which dimension will be

+plotted on the y-axis. If \code{reducedDimName} is not supplied, then this

+should be a vector which will be plotted on the y-axis. Default \code{2}.}

-\item{size}{Numeric. Sets size of point on plot. Default 1.}

+\item{size}{Numeric. Sets size of point on plot. Default \code{0.5}.}

-\item{xlab}{Character vector. Label for the x-axis. Default "Dimension_1".}

+\item{xlab}{Character vector. Label for the x-axis. Default \code{NULL}.}

-\item{ylab}{Character vector. Label for the y-axis. Default "Dimension_2".}

+\item{ylab}{Character vector. Label for the y-axis. Default \code{NULL}.}

 \item{specificClusters}{Numeric vector.

 Only color cells in the specified clusters.

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

 plotDimReduceFeature(

   x,

   features,

-  displayName = NULL,

   reducedDimName = NULL,

+  displayName = NULL,

   dim1 = NULL,

   dim2 = NULL,

   headers = NULL,

@@ -21,9 +21,9 @@ plotDimReduceFeature(

   exactMatch = TRUE,

   trim = c(-2, 2),

   limits = c(-2, 2),

-  size = 1,

-  xlab = "Dimension_1",

-  ylab = "Dimension_2",

+  size = 0.5,

+  xlab = NULL,

+  ylab = NULL,

   colorLow = "blue4",

   colorMid = "grey90",

   colorHigh = "firebrick1",

@@ -35,10 +35,10 @@ plotDimReduceFeature(

 \S4method{plotDimReduceFeature}{SingleCellExperiment}(

   x,

   features,

-  displayName = NULL,

   reducedDimName = NULL,

-  dim1 = NULL,

-  dim2 = NULL,

+  displayName = NULL,

+  dim1 = 1,

+  dim2 = 2,

   headers = NULL,

   useAssay = "counts",

   altExpName = "featureSubset",

@@ -47,9 +47,9 @@ plotDimReduceFeature(

   exactMatch = TRUE,

   trim = c(-2, 2),

   limits = c(-2, 2),

-  size = 1,

-  xlab = "Dimension_1",

-  ylab = "Dimension_2",

+  size = 0.5,

+  xlab = NULL,

+  ylab = NULL,

   colorLow = "blue4",

   colorMid = "grey90",

   colorHigh = "firebrick1",

@@ -69,7 +69,7 @@ plotDimReduceFeature(

   exactMatch = TRUE,

   trim = c(-2, 2),

   limits = c(-2, 2),

-  size = 1,

+  size = 0.5,

   xlab = "Dimension_1",

   ylab = "Dimension_2",

   colorLow = "blue4",

@@ -87,22 +87,26 @@ represent features and columns represent cells.}

 \item{features}{Character vector. Features in the rownames of counts to plot.}

+\item{reducedDimName}{The name of the dimension reduction slot in

+\code{reducedDimNames(x)} if \code{x} is a

+\linkS4class{SingleCellExperiment} object. If \code{NULL}, then both

+\code{dim1} and \code{dim2} need to be set. Default \code{NULL}.}

+

 \item{displayName}{Character. The column name of

 \code{rowData(x)} that specifies the display names for

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

 if \code{x} is a \linkS4class{SingleCellExperiment} object. Overwrites

 \code{headers}.}

-\item{reducedDimName}{The name of the dimension reduction slot in

-\code{reducedDimNames(x)} if \code{x} is a

-\linkS4class{SingleCellExperiment} object. If \code{NULL}, then both

-\code{dim1} and \code{dim2} need to be set. Default \code{NULL}.}

-

-\item{dim1}{Numeric vector. First dimension from data

-dimension reduction output to be plotted on the x-axis. Default \code{NULL}.}

+\item{dim1}{Integer or numeric vector. If \code{reducedDimName} is supplied,

+then, this will be used as an index to determine which dimension will be

+plotted on the x-axis. If \code{reducedDimName} is not supplied, then this

+should be a vector which will be plotted on the x-axis. Default \code{1}.}

-\item{dim2}{Numeric vector. Second dimension from data dimension

-reduction output to be plotted on the y-axis. Default \code{NULL}.}

+\item{dim2}{Integer or numeric vector. If \code{reducedDimName} is supplied,

+then, this will be used as an index to determine which dimension will be

+plotted on the y-axis. If \code{reducedDimName} is not supplied, then this

+should be a vector which will be plotted on the y-axis. Default \code{2}.}

 \item{headers}{Character vector. If \code{NULL}, the corresponding

 rownames are used as labels. Otherwise, these headers are used to label

@@ -76,7 +76,7 @@ row of the matrix will be plotted as a separate facet.}

 \linkS4class{SingleCellExperiment} object. Ignored if both \code{dim1} and

 \code{dim2} are set.}

-\item{dim1}{Numeric vector. First dimension from data dimension

+\item{dim1}{Numeric vector. Second dimension from data dimension

 reduction output.}

 \item{dim2}{Numeric vector. Second dimension from data dimension

@@ -10,17 +10,17 @@

 plotDimReduceModule(

   x,

   reducedDimName,

-  dim1 = NULL,

-  dim2 = NULL,

   useAssay = "counts",

   altExpName = "featureSubset",

   celdaMod,

   modules = NULL,

+  dim1 = NULL,

+  dim2 = NULL,

+  size = 0.5,

+  xlab = NULL,

+  ylab = NULL,

   rescale = TRUE,

   limits = c(0, 1),

-  size = 1,

-  xlab = "Dimension_1",

-  ylab = "Dimension_2",

   colorLow = "grey90",

   colorHigh = "firebrick1",

   ncol = NULL,

@@ -30,16 +30,16 @@ plotDimReduceModule(

 \S4method{plotDimReduceModule}{SingleCellExperiment}(

   x,

   reducedDimName,

-  dim1 = NULL,

-  dim2 = NULL,

   useAssay = "counts",

   altExpName = "featureSubset",

   modules = NULL,

+  dim1 = 1,

+  dim2 = 2,

+  size = 0.5,

+  xlab = NULL,

+  ylab = NULL,

   rescale = TRUE,

   limits = c(0, 1),

-  size = 1,

-  xlab = "Dimension_1",

-  ylab = "Dimension_2",

   colorLow = "grey90",

   colorHigh = "firebrick1",

   ncol = NULL,

@@ -48,15 +48,15 @@ plotDimReduceModule(

 \S4method{plotDimReduceModule}{ANY}(

   x,

-  dim1,

-  dim2,

   celdaMod,

   modules = NULL,

-  rescale = TRUE,

-  limits = c(0, 1),

-  size = 1,

+  dim1,

+  dim2,

+  size = 0.5,

   xlab = "Dimension_1",

   ylab = "Dimension_2",

+  rescale = TRUE,

+  limits = c(0, 1),

   colorLow = "grey90",

   colorHigh = "firebrick1",

   ncol = NULL,

@@ -73,12 +73,6 @@ represent features and columns represent cells.}

 \linkS4class{SingleCellExperiment} object. Ignored if both \code{dim1} and

 \code{dim2} are set.}

-\item{dim1}{Numeric vector.

-First dimension from data dimension reduction output.}

-

-\item{dim2}{Numeric vector.

-Second dimension from data dimension reduction output.}

-

 \item{useAssay}{A string specifying which \link{assay}

 slot to use if \code{x} is a

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

@@ -92,18 +86,28 @@ to use. Default "featureSubset".}

 \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.}

+\item{dim1}{Integer or numeric vector. If \code{reducedDimName} is supplied,

+then, this will be used as an index to determine which dimension will be

+plotted on the x-axis. If \code{reducedDimName} is not supplied, then this

+should be a vector which will be plotted on the x-axis. Default \code{1}.}

-\item{limits}{Passed to \link{scale_colour_gradient}. The range

-of color scale.}

+\item{dim2}{Integer or numeric vector. If \code{reducedDimName} is supplied,

+then, this will be used as an index to determine which dimension will be

+plotted on the y-axis. If \code{reducedDimName} is not supplied, then this

+should be a vector which will be plotted on the y-axis. Default \code{2}.}

-\item{size}{Numeric. Sets size of point on plot. Default 1.}

+\item{size}{Numeric. Sets size of point on plot. Default 0.5.}

 \item{xlab}{Character vector. Label for the x-axis. Default "Dimension_1".}

 \item{ylab}{Character vector. Label for the y-axis. Default "Dimension_2".}

+\item{rescale}{Logical.

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

+

+\item{limits}{Passed to \link{scale_colour_gradient}. The range

+of color scale.}

+

 \item{colorLow}{Character. A color available from `colors()`.

 The color will be used to signify the lowest values on the scale.}