Merge branch 'release/1.3.1'

.travis.yml

@@ -14,15 +14,15 @@ language: r
 cache: packages
 
 # R versions to be tested on
-r: 
+r:
   - bioc-release
   - bioc-devel
 
 ## Turn this to true before submission to CRAN/Bioconductor
 warnings_are_errors: false
 
-r_build_args: "--no-build-vignettes"
-r_check_args: "--no-vignettes"
+# r_build_args: "--no-build-vignettes"
+# r_check_args: "--no-vignettes"
 
 notifications:
   email:

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: clusterExperiment
 Title: Compare Clusterings for Single-Cell Sequencing 
-Version: 1.3.0
+Version: 1.3.1
 Description: Provides functionality for running and comparing many
     different clusterings of single-cell sequencing data or other large mRNA Expression data sets.
 Authors@R: c(person("Elizabeth", "Purdom", email = "epurdom@stat.berkeley.edu",
@@ -13,9 +13,9 @@ BugReports: https://github.com/epurdom/clusterExperiment/issues
 License: Artistic-2.0
 Depends:
     R (>= 3.3),
-    methods,
     SummarizedExperiment
 Imports:
+    methods,
     NMF,
     RColorBrewer,
     ape,
@@ -29,7 +29,8 @@ Imports:
     matrixStats,
     graphics,
     parallel,
-	MAST
+    MAST,
+    RSpectra
 Suggests:
     BiocStyle,
     knitr,

NAMESPACE

@@ -24,6 +24,7 @@ exportMethods("clusterTypes<-")
 exportMethods("coClustering<-")
 exportMethods("orderSamples<-")
 exportMethods("primaryClusterIndex<-")
+exportMethods("transformation<-")
 exportMethods(RSEC)
 exportMethods(addClusters)
 exportMethods(clusterContrasts)
@@ -39,6 +40,7 @@ exportMethods(clusterTypes)
 exportMethods(coClustering)
 exportMethods(combineMany)
 exportMethods(convertClusterLegend)
+exportMethods(dendroClusterIndex)
 exportMethods(getBestFeatures)
 exportMethods(makeDendrogram)
 exportMethods(mergeClusters)
@@ -73,6 +75,8 @@ importFrom(MAST,Hypothesis)
 importFrom(NMF,aheatmap)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(RColorBrewer,brewer.pal.info)
+importFrom(RSpectra,svds)
+importFrom(ape,phydataplot)
 importFrom(ape,plot.phylo)
 importFrom(cluster,daisy)
 importFrom(cluster,pam)
@@ -87,8 +91,13 @@ importFrom(matrixStats,rowVars)
 importFrom(parallel,mclapply)
 importFrom(phylobase,ancestors)
 importFrom(phylobase,descendants)
+importFrom(phylobase,edgeLength)
 importFrom(phylobase,getNode)
 importFrom(phylobase,labels)
+importFrom(phylobase,nNodes)
+importFrom(phylobase,nodeLabels)
+importFrom(phylobase,rootNode)
+importFrom(phylobase,subset)
 importFrom(stats,dist)
 importFrom(stats,hclust)
 importFrom(stats,mad)

NEWS

@@ -1,14 +1,39 @@
+Changes in version 1.3.1 ( Release date: 2017-06-14 )
+==============
+Changes:
+* change how `plotHeatmap` handles visualizeData argument, so not required to have same number of genes as original, only same number of samples. 
+* Now if color of vectors given in `clusterLegend` does not have names, `plotHeatmap` will give them names matching the variable so that they will be used by `aheatmap` (previously would have left all colors white because do not have matching names).
+* Large changes to how dendrograms are plotted by `plotDendrogram` and `mergeClusters`. This includes the ability to see the before and after clusterings along side the mergeClusters result, as well as a new slot added to the clusterExperiment class (`dendro_outbranch`). The names of several arguments to `mergeClusters` and `plotDendrogram` were changed for clarity: 
+	- `leaves` is now `leafType` in `plotDendrogram`. 
+	- `plotType` is now `plotInfo` in `mergeClusters`
+	- `doPlot` is now `plot` in `mergeClusters`
+	- `leafType` is now an option for `mergeClusters` as well.
+	- Now when `plotInfo` (previously `plotType`) is set to `none`, the plot is still drawn, but just no information about the merging is added to the plot. To not plot the dendrogram at all, set `plot=FALSE`.
+	- The option `labelType` in either `plotDendrogram` or `mergeClusters` controls whether names (`name`) or rectangular color blocks corresponding to the cluster (`colorblock`) are put at the tips of the dendrogram to label the clusters/samples. 
+* added `dendroClusterIndex` that behaves similarly to `primaryClusterIndex`
+* added ability to give `dendro` as charater option to `whichClusters` argument
+* added `transformation<-` to be able to assign manually the transformation slot
+* Move MAST into 'suggests' pacakge so that not need R 3.4 to run the package. 
+* Change calculation of PCA dimensionality reduction to use `svds` from `RSpectra` package to improve speed
+
+Bugs:
+* Fixed bug in RSEC where `combineProportion` argument was being ignored (set to 1)
+* Fixed bug in definition of `transform` so that extends existing generic rather than masking it.
+
 Changes in version 1.3.0 ( Release date: 2017-05-24  )
 ==============
 Changes:
 * `plotHeatmap` accepts `data.frame` or `ExpressionSet` objects for the data argument (calls `data.matrix` or `exprs` on object and sends to matrix version)
 * Added `plotBarplot` to plot a barplot for 1 cluster or comparison of 2 clusters along with tests.
 * Added `whichClusters` argument to `clusterMatrix` to return only clusters corresponding to certain clusters. Mainly relevant for using arguments like `workflow` that are used by other commands (otherwise could just index the complete matrix manually...)
 
+
 Bug fixes:
 * `plotHeatmap` now goes through the `clusterLegend` input and removes levels that do not exist in the sampleData; this was causing incorrect coloring when the `clusterLegend` had more (or less) levels that it assigned color to than the `sampleData` did (e.g. if `sampleData` was a subset of larger dataset upon which the original colors were assigned.) NOTE: that this now has the effect of NOT plotting all values in the clusterLegend if they are not represented in the data, thus changing the previous behavior of `plotHeatmap` legend.
 * fixed bug in how `plotHeatmap` checked that the dimensions of user-supplied dendrogram match that of data (matrix version).
 * fixed `convertClusterLegend` so when `output` is `matrixNames` or `matrixColors`, the resulting matrix has the `colnames` equal to cluster labels, like `clusterMatrix`.
+* internal function .convertToNum now preserves names of input vector. 
+* fixed bug in plotting with merge clusters; previously if plotType="all", might not have been correctly plotted with the right internal node of the dendrogram.
 
 Changes in version 1.2.0 ( Release date:  2017-04-04 )
 ==============

R/AllClasses.R

@@ -52,6 +52,8 @@ setClassUnion("matrixOrMissing",members=c("matrix", "missing"))
 #' details).
 #' @slot dendro_index numeric. An integer giving the cluster that was used to
 #'   make the dendrograms. NA_real_ value if no dendrograms are saved.
+#' @slot dendro_outbranch logical. Whether the dendro_samples dendrogram put 
+#' missing/non-clustered samples in an outbranch, or intermixed in the dendrogram.
 #' @slot coClustering matrix. A matrix with the cluster co-occurrence
 #' information; this can either be based on subsampling or on co-clustering
 #' across parameter sets (see \code{clusterMany}). The matrix is a square matrix
@@ -85,6 +87,7 @@ setClass(
     dendro_samples = "dendrogramOrNULL",
     dendro_clusters = "dendrogramOrNULL",
     dendro_index = "numeric",
+	dendro_outbranch = "logical",
     coClustering = "matrixOrNULL",
     clusterLegend="list",
     orderSamples="numeric"
@@ -129,32 +132,37 @@ setValidity("ClusterExperiment", function(object) {
   if(NCOL(object@clusterMatrix)!= length(object@clusterInfo)) {
     return("length of clusterInfo must be same as NCOL of the clusterMatrix")
   }
-
-  ##Check dendrograms
+  ############
+  ##Check dendrogram slotNames
+  ############
   #browser()
   if(!is.null(object@dendro_samples)){
     if(nobs(object@dendro_samples) != NCOL(object)) {
       return("dendro_samples must have the same number of leaves as the number of samples")
     }
+	if(is.na(object@dendro_outbranch)) return("if dendro_samples is defined, must also define dendro_outbranch")
   }
   else{
     if(!is.null(object@dendro_clusters)) return("dendro_samples should not be null if dendro_clusters is non-null")
+	if(!is.na(object@dendro_outbranch)) return("dendro_samples should not be null if dendro_outbranch is not NA")
   }
   if(!is.null(object@dendro_clusters)){
-    if(is.na(object@dendro_index)) return("if dendrogram slots are filled, must have corresponding dendro_index defined.")
-    dcluster<-clusterMatrix(object)[,object@dendro_index]
+    if(is.na(dendroClusterIndex(object))) return("if dendrogram slots are filled, must have corresponding dendro_index defined.")
+    dcluster<-clusterMatrix(object)[,dendroClusterIndex(object)]
     if(nobs(object@dendro_clusters) != max(dcluster)) {
       return("dendro_clusters must have the same number of leaves as the number of (non-negative) clusters")
     }
   }
   else{
     if(!is.null(object@dendro_samples)) return("dendro_clusters should not be null if dendro_samples is non-null")
   }
+  ## Check co-clustering
   if(!is.null(object@coClustering) &&
      (NROW(object@coClustering) != NCOL(object@coClustering)
       | NCOL(object@coClustering) != NCOL(object))) {
     return("`coClustering` must be a sample by sample matrix.")
   }
+  ## If have a cluster matrix
   if(!all(is.na(object@clusterMatrix))){ #what does this mean, how can they be all NA?
     #check primary index
     if(length(object@primaryIndex) != 1) {
@@ -331,6 +339,7 @@ setMethod(
 #'@param dendro_samples dendrogram. Sets the `dendro_samples` slot (see Slots).
 #'@param dendro_clusters dendrogram. Sets the `dendro_clusters` slot (see
 #'  Slots).
+#' @param dendro_outbranch logical. Sets the `dendro_outbranch` slot (see Slots)
 #'@param dendro_index numeric. Sets the dendro_index slot (see Slots).
 #'@param coClustering matrix. Sets the `coClustering` slot (see Slots).
 #'@details The \code{clusterExperiment} constructor function gives clusterLabels
@@ -348,6 +357,7 @@ setMethod(
             dendro_samples=NULL,
             dendro_index=NA_real_,
             dendro_clusters=NULL,
+			dendro_outbranch=NA,
             coClustering=NULL
             ){
     if(NCOL(se) != nrow(clusters)) {
@@ -396,6 +406,7 @@ setMethod(
                dendro_samples=dendro_samples,
                dendro_clusters=dendro_clusters,
                dendro_index=dendro_index,
+               dendro_outbranch=dendro_outbranch,
                coClustering=coClustering
     )
     validObject(out)

R/AllGenerics.R

@@ -192,13 +192,20 @@ setGeneric(
     standardGeneric("transformation")
   }
 )
-
 setGeneric(
-  name = "transform",
-  def = function(x,...) {
-    standardGeneric("transform")
+  name = "transformation<-",
+  def = function(object, value) {
+    standardGeneric("transformation<-")
   }
 )
+# don't need this because a standard generic already exists
+# setGeneric(
+#   name = "transform",
+#   def = function(x,...) {
+#     standardGeneric("transform")
+#   }
+# )
+setGeneric("transform")
 
 setGeneric(
   name = "clusterMatrix",
@@ -228,6 +235,12 @@ setGeneric(
   }
 )
 
+setGeneric(
+  name = "dendroClusterIndex",
+  def = function(x) {
+    standardGeneric("dendroClusterIndex")
+  }
+)
 setGeneric(
   name = "coClustering",
   def = function(x) {

R/AllHelper.R

@@ -91,7 +91,7 @@ setMethod(
     cat("Table of clusters (of primary clustering):")
     print(table(primaryClusterNamed(object)))
     cat("Total number of clusterings:", NCOL(clusterMatrix(object)),"\n")
-    if(!is.na(object@dendro_index) ) cat("Dendrogram run on '",clusterLabels(object)[object@dendro_index],"' (cluster index: ", object@dendro_index,")\n",sep="") else cat("No dendrogram present\n")
+    if(!is.na(dendroClusterIndex(object)) ) cat("Dendrogram run on '",clusterLabels(object)[dendroClusterIndex(object)],"' (cluster index: ", dendroClusterIndex(object),")\n",sep="") else cat("No dendrogram present\n")
     cat("-----------\n")
     cat("Workflow progress:\n")
     typeTab<-names(table(clusterTypes(object)))
@@ -148,6 +148,19 @@ setMethod(
   }
 )
 
+#' @rdname ClusterExperiment-methods
+#' @export
+#' @aliases transformation<-
+setReplaceMethod(
+  f = "transformation",
+  signature = signature("ClusterExperiment", "function"),
+  definition = function(object, value) {
+    object@transformation <- value
+    validObject(object)
+    return(object)
+  }
+)
+
 #' @rdname ClusterExperiment-methods
 #' @return \code{nClusters} returns the number of clusterings (i.e., ncol of
 #' clusterMatrix).
@@ -252,6 +265,20 @@ setMethod(
   }
 )
 
+#' @rdname ClusterExperiment-methods
+#' @return \code{dendroClusterIndex} returns/sets the clustering index 
+#' of the clusters used to create dendrogram
+#' (i.e., which column of clusterMatrix corresponds to the clustering).
+#' @export
+#' @aliases dendroClusterIndex
+setMethod(
+  f = "dendroClusterIndex",
+  signature = "ClusterExperiment",
+  definition = function(x) {
+    return(x@dendro_index)
+  }
+)
+
 #' @rdname ClusterExperiment-methods
 #' @export
 #' @aliases primaryClusterIndex<-

R/addClusters.R

@@ -118,15 +118,17 @@ setMethod(
     newClusterColors<-clusterLegend(x)[-whichRemove]
     dend_samples <- x@dendro_samples
     dend_cl <- x@dendro_clusters
-    dend_ind<-x@dendro_index
+    dend_ind<-dendroClusterIndex(x)
+    dend_out<-x@dendro_outbranch
     coMat<-x@coClustering
     orderSamples<-orderSamples(x)
     if(primaryClusterIndex(x) %in% whichRemove) pIndex<-1
     else pIndex<-match(primaryClusterIndex(x),(1:NCOL(clusterMatrix(x)))[-whichRemove])
-    if(x@dendro_index %in% whichRemove){
+    if(dendroClusterIndex(x) %in% whichRemove){
         dend_cl<-NULL
         dend_samples<-NULL
         dend_ind<-NA_real_
+        dend_out<-NA
     }
     else{
       dend_ind<-match(dend_ind,(1:NCOL(clusterMatrix(x)))[-whichRemove])
@@ -139,6 +141,7 @@ setMethod(
                               dendro_samples=dend_samples,
                               dendro_clusters=dend_cl,
                             dendro_index=dend_ind,
+                            dendro_outbranch=dend_out,
                             coClustering=coMat,
                             orderSamples=orderSamples
                               )