Merge pull request #210 from rcastelo/200-store-internal-gsva-ranks-t…

…o-enable-enrichment-plots-and-flexible-scoring

200 store internal gsva ranks to enable enrichment plots and flexible scoring

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export("geneSets<-")
 export("gsvaAnnotation<-")
 export(computeGeneSetsOverlap)
 export(deduplicateGeneSets)
@@ -9,7 +10,10 @@ export(geneSetSizes)
 export(geneSets)
 export(gsva)
 export(gsvaAnnotation)
+export(gsvaEnrichment)
 export(gsvaParam)
+export(gsvaRanks)
+export(gsvaScores)
 export(guessGeneIdType)
 export(igsva)
 export(plageParam)
@@ -21,6 +25,7 @@ exportClasses(GsvaExprData)
 exportClasses(GsvaGeneSets)
 exportClasses(GsvaMethodParam)
 exportClasses(gsvaParam)
+exportClasses(gsvaRanksParam)
 exportClasses(plageParam)
 exportClasses(ssgseaParam)
 exportClasses(zscoreParam)
@@ -30,6 +35,8 @@ exportMethods(geneSetSizes)
 exportMethods(geneSets)
 exportMethods(gsva)
 exportMethods(gsvaAnnotation)
+exportMethods(gsvaRanks)
+exportMethods(gsvaScores)
 exportMethods(spatCor)
 import(methods)
 importClassesFrom(Biobase,ExpressionSet)
@@ -80,13 +87,18 @@ importFrom(SpatialExperiment,SpatialExperiment)
 importFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(SummarizedExperiment,assay)
 importFrom(cli,cli_abort)
+importFrom(cli,cli_alert_danger)
 importFrom(cli,cli_alert_info)
 importFrom(cli,cli_alert_success)
 importFrom(cli,cli_alert_warning)
 importFrom(cli,cli_progress_bar)
 importFrom(cli,cli_progress_done)
 importFrom(cli,cli_progress_update)
+importFrom(graphics,abline)
+importFrom(graphics,grid)
+importFrom(graphics,lines)
 importFrom(graphics,plot)
+importFrom(graphics,segments)
 importFrom(methods,new)
 importFrom(parallel,splitIndices)
 importFrom(sparseMatrixStats,colRanks)
@@ -99,6 +111,7 @@ importFrom(stats,rnorm)
 importFrom(stats,rpois)
 importFrom(stats,sd)
 importFrom(utils,capture.output)
+importFrom(utils,globalVariables)
 importFrom(utils,head)
 importFrom(utils,installed.packages)
 importFrom(utils,packageDescription)

R/AllClasses.R

@@ -336,3 +336,21 @@ setClass("gsvaParam",
                         maxDiff=NA,
                         absRanking=NA,
                         sparse=FALSE))
+
+#' @name gsvaRanksParam-class
+#' @rdname gsvaParam-class
+#' @exportClass gsvaRanksParam
+setClass("gsvaRanksParam",
+         contains="gsvaParam",
+         prototype=list(exprData=NULL,
+                        geneSets=NULL,
+                        assay=NA_character_,
+                        annotation=NULL,
+                        minSize=NA_integer_,
+                        maxSize=NA_integer_,
+                        kcdf=NA_character_,
+                        kcdfNoneMinSampleSize=NA_integer_,
+                        tau=NA_real_,
+                        maxDiff=NA,
+                        absRanking=NA,
+                        sparse=FALSE))

R/AllGenerics.R

@@ -3,6 +3,18 @@
 setGeneric("gsva",
            function(param, ...) standardGeneric("gsva"))
 
+#' @export 
+setGeneric("gsvaRanks",
+           function(param, ...) standardGeneric("gsvaRanks"))
+
+#' @export 
+setGeneric("gsvaScores",
+           function(param, ...) standardGeneric("gsvaScores"))
+
+#' @export 
+setGeneric("gsvaEnrichment",
+           function(param, ranks, ...) standardGeneric("gsvaEnrichment"))
+
 #' @export 
 setGeneric("filterGeneSets",
            function(gSets, ...) standardGeneric("filterGeneSets"))
@@ -15,6 +27,10 @@ setGeneric("computeGeneSetsOverlap",
 setGeneric("geneSets",
            function(obj, ...) standardGeneric("geneSets"))
 
+#' @export
+setGeneric("geneSets<-",
+           function(object, value) standardGeneric("geneSets<-"))
+
 #' @export
 setGeneric("geneSetSizes",
            function(obj, ...) standardGeneric("geneSetSizes"))

R/GSVA-package.R

@@ -28,7 +28,6 @@
 #' @importFrom BiocParallel SerialParam MulticoreParam multicoreWorkers bpnworkers
 #' @importFrom SingleCellExperiment SingleCellExperiment
 #' @importFrom SpatialExperiment SpatialExperiment
-#' @importFrom sparseMatrixStats colRanks rowRanges
 #' @importFrom DelayedArray rowAutoGrid colAutoGrid defaultAutoGrid
 #' currentBlockId read_block gridReduce write_block close t colSums
 #' @importFrom HDF5Array HDF5RealizationSink writeHDF5Array