merging release into master

.Rbuildignore

@@ -3,7 +3,6 @@
 ^.svn
 ^.git
 README[.]md
-NEWS[.]md
 
 # Travis-CI et al.
 ^[.]travis[.]yml$
@@ -30,3 +29,4 @@ NEWS[.]md
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.\./inst/NEWS$
+^tests/checkClusterMany/*$

.gitignore

@@ -4,5 +4,10 @@
 vignettes/figure
 *.Rproj
 clusterVignette.md
-vignettes/R_cache
-vignettes/R_figure
+vignettes/*_cache
+vignettes/*_figure
+vignettes/*.R
+tests/checkClusterMany/*.Rout
+tests/checkClusterMany/*.txt
+tests/checkClusterMany/nohup.out
+tests/checkClusterMany/*.tar.gz

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: clusterExperiment
 Title: Compare clusterings for single-cell sequencing
-Version: 0.99.2
+Version: 0.99.3
 Description: This package provides functions for running and comparing many
     different clusterings of single-cell sequencing data.
 Authors@R: c(person("Elizabeth", "Purdom", email = "epurdom@stat.berkeley.edu",
@@ -34,7 +34,7 @@ Suggests:
     knitr,
     diagram,
     testthat,
-    scRNAseq
+	scRNAseq
 VignetteBuilder: knitr
 LazyData: true
 RoxygenNote: 5.0.1

NAMESPACE

@@ -22,6 +22,7 @@ exportMethods("clusterTypes<-")
 exportMethods("coClustering<-")
 exportMethods("orderSamples<-")
 exportMethods("primaryClusterIndex<-")
+exportMethods(RSEC)
 exportMethods(addClusters)
 exportMethods(clusterContrasts)
 exportMethods(clusterExperiment)
@@ -86,3 +87,7 @@ importFrom(phylobase,getNode)
 importFrom(phylobase,labels)
 importFrom(stats,dist)
 importFrom(stats,hclust)
+importFrom(stats,mad)
+importFrom(stats,prcomp)
+importFrom(stats,sd)
+importFrom(stats,var)

NEWS

@@ -1,3 +1,34 @@
+Changes in version 0.99.1-9000 (Release date:  )
+==============
+
+Changes:
+* plot in mergeClusters now uses cluster names and colors from clusterLegend
+* plotDendrogram now calls plot.phylo
+* add 'clusterLabel' argument to `clusterSingle`
+* add options 'mad' and 'cv' to the dimensionality reduction. Also made option to only use clustered samples for feature reduction for relevant functions (e.g. `makeDendrogram`).
+* clusterSingle now always returns the D matrix to the slot coClustering (previously only did so if D was from subsampling).
+* change so that clusterSingle takes dissimilarity matrix, and now clusterMany calculates dissimilarities up front (rather than recalculating each time)
+* add RSEC function for wrapper that leads to RSEC algorithm.
+* add test for clusterMany to make sure replicable with past results (not unit test because too long to run, so not part of R build)
+
+Bug fixes:
+* fix bug in .TypeIntoIndices so that handles mix of clusterType and clusterLabels in whichClusters
+* fixed bug in plotCoClustering so handles clusterSamplesData
+* D for clusterD is now distance, not similarity, for 0-1, meaning larger values are values that are less similar.
+* fix bug in plotClusters that would give clusterLegend entries that were vectors, not matrices.
+
+Changes in version 0.99.1 (Release date: 2016-05-24 )
+==============
+
+Changes:
+* changes to pass development version of bioConductor checks.
+
+Changes in version 0.99.0 (Release date: 2016-05-24 )
+==============
+
+Changes:
+* changed number to indicate bioconductor submission
+
 Changes in version 0.2.0 (Release date: 2016-05-10 )
 ==============
 

R/AllClasses.R

@@ -1,6 +1,7 @@
 setOldClass("dendrogram")
 setClassUnion("dendrogramOrNULL",members=c("dendrogram", "NULL"))
 setClassUnion("matrixOrNULL",members=c("matrix", "NULL"))
+setClassUnion("matrixOrMissing",members=c("matrix", "missing"))
 #' @title Class ClusterExperiment
 #'
 #' @description \code{ClusterExperiment} is a class that extends
@@ -331,6 +332,9 @@ setMethod(
 #'  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
+#'  based on the column names of the input matrix/SummarizedExperiment. If
+#'  missing, will assign labels "cluster1","cluster2", etc.
 setMethod(
   f = "clusterExperiment",
   signature = signature("SummarizedExperiment","matrix"),

R/AllGenerics.R

@@ -1,6 +1,13 @@
+setGeneric(
+    name = "RSEC",
+    def = function(x, ...) {
+        standardGeneric("RSEC")
+    }
+)
+
 setGeneric(
   name = "clusterSingle",
-  def = function(x,  ...) {
+  def = function(x, diss,  ...) {
     standardGeneric("clusterSingle")
   }
 )