@@ -2,3 +2,5 @@

 ^\.Rproj\.user$

 ^CONDUCT\.md$

 .travis.yml

+NOTICE

+_pkgdown.yml

@@ -50,13 +50,13 @@ Imports:

     scater (>= 1.14.4),

     scran,

     SingleCellExperiment,

-    dbscan

+    dbscan,

+    DelayedArray

 Suggests:

     testthat,

     knitr,

     roxygen2,

     rmarkdown,

-    corrplot,

     Matrix,

     biomaRt,

     covr,

@@ -58,6 +58,10 @@

 #'  Default TRUE.

 #' @param showNamesCell Logical. Specifies if cell names should be shown.

 #'  Default FALSE.

+#' @param rowGroupOrder Vector. Specifies the order of feature clusters when 

+#'  semisupervised clustering is performed on the \code{y} labels.

+#' @param colGroupOrder Vector. Specifies the order of cell clusters when 

+#'  semisupervised clustering is performed on the \code{z} labels.

 #' @param hclustMethod Character. Specifies the method to use for the 'hclust'

 #'  function. See `?hclust` for possible values. Default "ward.D2".

 #' @param treeheightFeature Numeric. Width of the feature dendrogram. Set to 0

@@ -79,8 +83,6 @@

 plotHeatmap <- function(counts,

     z = NULL,

     y = NULL,

-    rowGroupOrder = NULL,

-    colGroupOrder = NULL,

     scaleRow = scale,

     trim = c(-2, 2),

     featureIx = NULL,

@@ -101,6 +103,8 @@ plotHeatmap <- function(counts,

     annotationNamesCell = TRUE,

     showNamesFeature = FALSE,

     showNamesCell = FALSE,

+    rowGroupOrder = NULL,

+    colGroupOrder = NULL,

     hclustMethod = "ward.D2",

     treeheightFeature = ifelse(clusterFeature, 50, 0),

     treeheightCell = ifelse(clusterCell, 50, 0),

@@ -45,6 +45,7 @@

 #' @param logfile Character. Messages will be redirected to a file named

 #'  `logfile`. If NULL, messages will be printed to stdout.  Default NULL.

 #' @param verbose Logical. Whether to print log messages. Default TRUE.

+#' @param ... For the generic, further arguments to pass to each method.

 #'

 #' @return If \code{x} is a matrix-like object, a list will be returned

 #' with the following items:

@@ -153,7 +154,7 @@ setMethod("decontX", "SingleCellExperiment", function(x,

   ## Save the rest of the result object into metadata

   decontXcounts(x) <- result$decontXcounts

   result$decontXcounts <- NULL

-  metadata(x)$decontX <- result

+  S4Vectors::metadata(x)$decontX <- result

   return(x)

 })

@@ -208,12 +209,27 @@ SET_FUN <- function(exprs_values, ...) {

   }

 }

+

+

+#' @title Get or set decontaminated counts matrix

+#'

+#' @description Gets or sets the decontaminated counts matrix from a

+#' a \linkS4class{SingleCellExperiment} object.

+#' @name decontXcounts

+#' @param object A \linkS4class{SingleCellExperiment} object.

+#' @param value A matrix to save as an assay called \code{decontXcounts} 

+#' @param ... For the generic, further arguments to pass to each method.

+#' @seealso \code{\link{assay}} and \code{\link{assay<-}}

+NULL

+

 #' @export

+#' @rdname decontXcounts

 setGeneric("decontXcounts", function(object, ...) {

   standardGeneric("decontXcounts")

 })

 #' @export

+#' @rdname decontXcounts

 setGeneric("decontXcounts<-", function(object, ..., value) {

   standardGeneric("decontXcounts<-")

 })

@@ -339,7 +355,7 @@ setReplaceMethod(

         append = TRUE,

         verbose = verbose

       )

-      countsBat <- as(countsBat, "dgCMatrix")

+      countsBat <- methods::as(countsBat, "dgCMatrix")

     }

@@ -440,19 +456,19 @@ setReplaceMethod(

     ## Determine class of seed in DelayedArray

     seed.class <- unique(DelayedArray::seedApply(counts, class))[[1]]

     if (seed.class == "HDF5ArraySeed") {

-      returnResult$decontXcounts <- as(returnResult$decontXcounts, "HDF5Matrix")

+      returnResult$decontXcounts <- methods::as(returnResult$decontXcounts, "HDF5Matrix")

     } else {

-      if (isTRUE(canCoerce(returnResult$decontXcounts, seed.class))) {

-        returnResult$decontXcounts <- as(returnResult$decontXcounts, seed.class)

+      if (isTRUE(methods::canCoerce(returnResult$decontXcounts, seed.class))) {

+        returnResult$decontXcounts <- methods::as(returnResult$decontXcounts, seed.class)

       }

     }

     returnResult$decontXcounts <-

       DelayedArray::DelayedArray(returnResult$decontXcounts)

   } else {

     try({

-        if (canCoerce(returnResult$decontXcounts, class(counts))) {

+        if (methods::canCoerce(returnResult$decontXcounts, class(counts))) {

           returnResult$decontXcounts <-

-            as(returnResult$decontXcounts, class(counts))

+            methods::as(returnResult$decontXcounts, class(counts))

         }

       },

       silent = TRUE

@@ -152,7 +152,8 @@ plotDendro <- function(decisionTree,

     suppressMessages(dendroP <- ggdendro::ggdendrogram(dendro) +

             ggplot2::geom_label(

                 data = dendSegsLabelled,

-                ggplot2::aes(x = xend, y = y, label = label),

+                ggplot2::aes(x = dendSegsLabelled$xend, y = dendSegsLabelled$y,

+                             label = dendSegsLabelled$label),

                 size = boxSize,

                 label.size = 1,

                 fontface = "bold",

@@ -447,7 +447,7 @@ plotDimReduceCluster <- function(dim1,

         ggplot2::guides(color =

                 ggplot2::guide_legend(override.aes = list(size = 1)))

-    if (labelClusters == TRUE) {

+    if (isTRUE(labelClusters)) {

         #centroidList <- lapply(seq(length(unique(cluster))), function(x) {

         centroidList <- lapply(unique(cluster), function(x) {

             df.sub <- df[df$Cluster == x, ]

@@ -467,7 +467,7 @@ plotDimReduceCluster <- function(dim1,

             size = 0,

             alpha = 0) +

             ggrepel::geom_text_repel(data = centroid,

-                mapping = ggplot2::aes(label = Cluster),

+                mapping = ggplot2::aes(label = centroid$Cluster),

                 size = labelSize)

     }

     if (!is.null(x = groupBy)) {

@@ -1401,6 +1401,10 @@ vplayout <- function(x, y) {

 #' @param silent do not draw the plot (useful when using the gtable output)

 #' @param rowLabel row cluster labels for semi-clustering

 #' @param colLabel column cluster labels for semi-clustering

+#' @param rowGroupOrder Vector. Specifies the order of feature clusters when 

+#'  semisupervised clustering is performed on the \code{y} labels.

+#' @param colGroupOrder Vector. Specifies the order of cell clusters when 

+#'  semisupervised clustering is performed on the \code{z} labels.

 #' @param \dots graphical parameters for the text used in plot. Parameters

 #'  passed to \code{\link{grid.text}}, see \code{\link{gpar}}.

 #' @return

@@ -1627,8 +1631,7 @@ semiPheatmap <- function(mat,

             mat <- mat[o, , drop = FALSE]

             fmat <- fmat[o, , drop = FALSE]

             rowLabel <- rowLabel[o]

-            if (!is.null(annotationRow) && length(annotationRow) > 0

-                && !is.na(annotationRow)) {

+            if (!is.null(annotationRow) && !is.null(ncol(annotationRow))) {

                 annotationRow <- annotationRow[o, , drop = FALSE]

             }

         }

@@ -1641,8 +1644,7 @@ semiPheatmap <- function(mat,

         mat <- mat[treeRow$order, , drop = FALSE]

         fmat <- fmat[treeRow$order, , drop = FALSE]

         labelsRow <- labelsRow[treeRow$order]

-        if (!is.null(annotationRow) && length(annotationRow) > 0

-            && !is.na(annotationRow)) {

+        if (!is.null(annotationRow) && !is.null(ncol(annotationRow))) {

           annotationRow <- annotationRow[treeRow$order, , drop = FALSE]

         }

         if (!is.na(cutreeRows)) {

@@ -1666,8 +1668,7 @@ semiPheatmap <- function(mat,

             mat <- mat[, o, drop = FALSE]

             fmat <- fmat[, o, drop = FALSE]

             colLabel <- colLabel[o]

-            if (!is.null(annotationCol) && length(annotationCol) > 0

-                && !is.na(annotationCol)) {

+            if (!is.null(annotationCol) && !is.null(ncol(annotationCol))) {

                 annotationCol <- annotationCol[o, , drop = FALSE]

             }

         }

@@ -1682,8 +1683,7 @@ semiPheatmap <- function(mat,

         fmat <- fmat[, treeCol$order, drop = FALSE]

         labelsCol <- labelsCol[treeCol$order]

-        if (!is.null(annotationCol) && length(annotationCol) > 0

-            && !is.na(annotationCol)) {

+        if (!is.null(annotationCol) && !is.null(ncol(annotationCol))) {

           annotationCol <- annotationCol[treeCol$order, , drop = FALSE]

         }

         if (!is.na(cutreeCols)) {

@@ -93,6 +93,8 @@ a default value of 12345 is used. If NULL, no calls to

 `logfile`. If NULL, messages will be printed to stdout.  Default NULL.}

 \item{verbose}{Logical. Whether to print log messages. Default TRUE.}

+

+\item{...}{For the generic, further arguments to pass to each method.}

 }

 \value{

 If \code{x} is a matrix-like object, a list will be returned

new file mode 100644

@@ -0,0 +1,25 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/decon.R

+\name{decontXcounts}

+\alias{decontXcounts}

+\alias{decontXcounts<-}

+\title{Get or set decontaminated counts matrix}

+\usage{

+decontXcounts(object, ...)

+

+decontXcounts(object, ...) <- value

+}

+\arguments{

+\item{object}{A \linkS4class{SingleCellExperiment} object.}

+

+\item{...}{For the generic, further arguments to pass to each method.}

+

+\item{value}{A matrix to save as an assay called \code{decontXcounts}}

+}

+\description{

+Gets or sets the decontaminated counts matrix from a

+a \linkS4class{SingleCellExperiment} object.

+}

+\seealso{

+\code{\link{assay}} and \code{\link{assay<-}}

+}

@@ -8,8 +8,6 @@ plotHeatmap(

   counts,

   z = NULL,

   y = NULL,

-  rowGroupOrder = NULL,

-  colGroupOrder = NULL,

   scaleRow = scale,

   trim = c(-2, 2),

   featureIx = NULL,

@@ -30,6 +28,8 @@ plotHeatmap(

   annotationNamesCell = TRUE,

   showNamesFeature = FALSE,

   showNamesCell = FALSE,

+  rowGroupOrder = NULL,

+  colGroupOrder = NULL,

   hclustMethod = "ward.D2",

   treeheightFeature = ifelse(clusterFeature, 50, 0),

   treeheightCell = ifelse(clusterCell, 50, 0),

@@ -118,6 +118,12 @@ Default TRUE.}

 \item{showNamesCell}{Logical. Specifies if cell names should be shown.

 Default FALSE.}

+\item{rowGroupOrder}{Vector. Specifies the order of feature clusters when 

+semisupervised clustering is performed on the \code{y} labels.}

+

+\item{colGroupOrder}{Vector. Specifies the order of cell clusters when 

+semisupervised clustering is performed on the \code{z} labels.}

+

 \item{hclustMethod}{Character. Specifies the method to use for the 'hclust'

 function. See `?hclust` for possible values. Default "ward.D2".}

@@ -203,6 +203,12 @@ unless specified otherwise.}

 \item{colLabel}{column cluster labels for semi-clustering}

+\item{rowGroupOrder}{Vector. Specifies the order of feature clusters when 

+semisupervised clustering is performed on the \code{y} labels.}

+

+\item{colGroupOrder}{Vector. Specifies the order of cell clusters when 

+semisupervised clustering is performed on the \code{z} labels.}

+

 \item{\dots}{graphical parameters for the text used in plot. Parameters

 passed to \code{\link{grid.text}}, see \code{\link{gpar}}.}

 }