Merge branch 'ADT' into staging

Author: deto

.Rbuildignore

@@ -3,4 +3,5 @@
 ^\.travis\.yml$
 ^build_whitelist.sh$
 ^docs/.*$
+^vignettes/web_only/.*$
 ^.*.eslintrc.json

.travis.yml

@@ -11,6 +11,11 @@ r:
 
 sudo: false
 
+addons:
+    apt:
+        packages:
+            - libhdf5-dev
+
 ## Turn this to true before submission to CRAN/Bioconductor
 warnings_are_errors: false
 

DESCRIPTION

@@ -12,6 +12,7 @@ Depends: R (>= 3.4)
 Imports:
 	fastICA,
 	igraph,
+    irlba,
 	jsonlite,
 	loe,
 	logging,
@@ -21,8 +22,10 @@ Imports:
 	matrixStats,
 	mclust,
 	methods,
+    mime,
     plumber,
-	Rcpp,
+    RANN,
+	Rcpp (>= 1.0.0),
 	rsvd,
 	stats,
 	Rtsne,
@@ -39,10 +42,13 @@ RoxygenNote: 6.1.1
 Suggests:
 	Biobase,
 	BiocStyle,
+    ggplot2,
+    hdf5r,
 	knitr,
 	rmarkdown,
+    SummarizedExperiment,
     testthat,
-    ggplot2
+    uwot
 biocViews:
 	GeneExpression,
 	RNASeq,

NAMESPACE

@@ -1,14 +1,24 @@
 # Generated by roxygen2: do not edit by hand
 
 export(Vision)
+export(addSignatures)
+export(addTSNE)
+export(addUMAP)
+export(analyzeLocalCorrelations)
+export(annotateLatentComponents)
 export(applyMicroClustering)
+export(calcSignatureScores)
+export(clusterSigScores)
+export(computeLatentSpace)
 export(convertGeneIds)
 export(createGeneSignature)
 export(poolMatrixCols)
 export(poolMatrixRows)
 export(poolMetaData)
 export(read_10x)
 export(read_10x_h5)
+export(read_10x_h5_v2)
+export(read_10x_h5_v3)
 exportMethods(Vision)
 exportMethods(addProjection)
 exportMethods(analyze)
@@ -28,13 +38,17 @@ import(Rcpp)
 import(loe)
 import(logging)
 import(methods)
-import(stats)
+importFrom(Matrix,Diagonal)
+importFrom(Matrix,Matrix)
+importFrom(Matrix,colMeans)
+importFrom(Matrix,colSums)
 importFrom(Matrix,readMM)
 importFrom(Matrix,rowMeans)
 importFrom(Matrix,rowSums)
 importFrom(Matrix,sparseMatrix)
 importFrom(Matrix,summary)
 importFrom(Matrix,tcrossprod)
+importFrom(RANN,nn2)
 importFrom(Rcpp,evalCpp)
 importFrom(Rcpp,sourceCpp)
 importFrom(Rtsne,Rtsne)
@@ -48,6 +62,7 @@ importFrom(igraph,layout_as_tree)
 importFrom(igraph,layout_with_dh)
 importFrom(igraph,layout_with_fr)
 importFrom(igraph,layout_with_mds)
+importFrom(irlba,irlba)
 importFrom(jsonlite,fromJSON)
 importFrom(jsonlite,toJSON)
 importFrom(matrixStats,colCounts)
@@ -56,31 +71,38 @@ importFrom(matrixStats,colMeans2)
 importFrom(matrixStats,colMedians)
 importFrom(matrixStats,colRanks)
 importFrom(matrixStats,colSds)
+importFrom(matrixStats,colVars)
 importFrom(matrixStats,logSumExp)
 importFrom(matrixStats,rowMaxs)
 importFrom(matrixStats,rowMeans2)
 importFrom(matrixStats,rowSds)
+importFrom(matrixStats,rowVars)
 importFrom(mclust,Mclust)
 importFrom(mclust,mclustBIC)
+importFrom(mime,guess_type)
 importFrom(parallel,mclapply)
 importFrom(pbmcapply,pbmclapply)
 importFrom(plumber,forward)
 importFrom(plumber,plumber)
 importFrom(rsvd,rsvd)
 importFrom(stats,chisq.test)
+importFrom(stats,cor.test)
+importFrom(stats,dist)
+importFrom(stats,hclust)
 importFrom(stats,kmeans)
 importFrom(stats,median)
-importFrom(stats,optim)
 importFrom(stats,p.adjust)
 importFrom(stats,pnorm)
-importFrom(stats,prcomp)
 importFrom(stats,quantile)
+importFrom(stats,rnorm)
+importFrom(stats,runif)
 importFrom(stats,sd)
+importFrom(stats,setNames)
 importFrom(stats,var)
 importFrom(utils,URLdecode)
 importFrom(utils,browseURL)
+importFrom(utils,read.table)
 importFrom(utils,stack)
-importFrom(utils,tail)
 importFrom(vegan,isomap)
 importFrom(wordspace,dist.matrix)
 useDynLib(VISION)

R/AllClasses.R

@@ -5,8 +5,10 @@
 # scores, distance matrices, and anything else, is computed
 # on the different types of data.
 
-setClassUnion('numericORNULL', members=c('numeric', 'NULL'))
-setClassUnion('matrixORSparse', members=c("matrix", "dgeMatrix", "dgCMatrix", "dgTMatrix"))
+setClassUnion("numericORNULL", members = c("numeric", "NULL"))
+setClassUnion("matrixORSparse", members = c("matrix", "dgCMatrix"))
+setClassUnion("matrixORNULL", members = c("matrix", "NULL"))
+setClassUnion("dataframeORNULL", members = c("data.frame", "NULL"))
 
 Cluster <- setClass("Cluster",
     slots = c(
@@ -17,16 +19,35 @@ Cluster <- setClass("Cluster",
     )
 )
 
-ProjectionData <- setClass("ProjectionData",
+NormData <- setClass("NormData",
     slots = c(
-    Consistency = "matrix",
-    pValue = "matrix",
-    FDR = "matrix",
-    sigClusters = "list"
-))
+    colOffsets = "numeric",
+    colScaleFactors = "numeric",
+    rowOffsets = "numeric",
+    rowScaleFactors = "numeric",
+    data = "Matrix"
+    ),
+    validity = function(object){
+        isValid <- nrow(object@data) == length(object@rowOffsets)
+
+        isValid <- isValid && (
+            nrow(object@data) == length(object@rowScaleFactors))
+
+        isValid <- isValid && (
+            ncol(object@data) == length(object@colOffsets))
+
+        isValid <- isValid && (
+            ncol(object@data) == length(object@colScaleFactors))
 
-PCAnnotatorData <- setClass("PCAnnotatorData",
-    slots = c(pearsonCorr = "matrix")
+        return(isValid)
+    },
+)
+
+LCAnnotatorData <- setClass("LCAnnotatorData",
+    slots = c(
+        pearsonCorr = "matrix",
+        pearsonCorrProteins = "matrixORNULL"
+    )
 )
 
 Trajectory <- setClass("Trajectory",
@@ -71,72 +92,48 @@ Signature <- setClass("Signature",
     metaData = ""
 ))
 
-setClassUnion("ProjectionDataOrNULL", members=c("ProjectionData", "NULL"))
-setClassUnion("PCAnnotatorDataOrNULL", members=c("PCAnnotatorData", "NULL"))
+setClassUnion("LCAnnotatorDataOrNULL", members=c("LCAnnotatorData", "NULL"))
 
 Vision <- setClass("Vision",
     slots = c(
-        nomodel = "logical",
-        projection_genes = "character",
-        weights = "matrix",
-        threshold = "numeric",
-        sig_norm_method = "character",
-        sig_score_method = "character",
         exprData = "matrixORSparse",
+        proteinData = "matrixORSparse",
         unnormalizedData = "matrixORSparse",
-        housekeepingData = "character",
         sigData = "list",
         metaData = "data.frame",
-        perm_wPCA = "logical",
-        pool = "logical",
-        sigScores = "matrix",
-        cellsPerPartition = "numeric",
-        SigConsistencyScores = "ProjectionDataOrNULL",
-        ClusterSigScores = "list",
-        TrajectoryConsistencyScores = "ProjectionDataOrNULL",
-        PCAnnotatorData = "PCAnnotatorDataOrNULL",
-        projection_methods = "character",
+        SigScores = "matrix",
+        LocalAutocorrelation = "list",
+        TrajectoryAutocorrelation = "list",
+        ClusterComparisons = "list",
+        LCAnnotatorData = "LCAnnotatorDataOrNULL",
         Projections = "list",
         TrajectoryProjections = "list", # list of TrajectoryProjection
         SigGeneImportance = "list",
-        pools = "list",
-        inputProjections = "list",
-        name = "character",
-        num_neighbors = "numericORNULL",
-        latentSpace = "matrix",
-        latentTrajectory = "Trajectory",
-        version = "numeric",
-        selections = "list",
-        params = "list"),
+        Pools = "list",
+        LatentSpace = "matrix",
+        LatentTrajectory = "Trajectory",
+        Viewer = "list",
+        params = "list",
+        version = "numeric"
+        ),
     prototype = list(
-        nomodel = FALSE,
-        weights = matrix(NA, 1, 1),
-        threshold = 0,
-        sig_norm_method = "znorm_rows",
         exprData = matrix(NA, 1, 1),
+        proteinData = matrix(NA, 1, 1),
         unnormalizedData = matrix(NA, 1, 1),
-        housekeepingData = character(),
         sigData = list(),
         metaData = data.frame(),
-        perm_wPCA = FALSE,
-        pool = FALSE,
-        sigScores = matrix(NA, 1, 1),
-        cellsPerPartition = 100,
-        SigConsistencyScores = NULL,
-        ClusterSigScores = list(),
-        TrajectoryConsistencyScores = NULL,
-        PCAnnotatorData = NULL,
-        projection_methods = character(),
+        SigScores = matrix(NA, 1, 1),
+        LocalAutocorrelation = list(),
+        TrajectoryAutocorrelation = list(),
+        ClusterComparisons = list(),
+        LCAnnotatorData = NULL,
         Projections = list(),
         TrajectoryProjections = list(),
         SigGeneImportance = list(),
-        pools = list(),
-        inputProjections = list(),
-        name = "",
-        num_neighbors = NULL, 
-        latentSpace = matrix(NA, 1, 1),
-        latentTrajectory = NULL,
-        version = 1.11,
-        selections = list(),
-        params = list()
+        Pools = list(),
+        LatentSpace = matrix(NA, 1, 1),
+        LatentTrajectory = NULL,
+        Viewer = list(),
+        params = list(),
+        version = 1.2
 ))

R/AllGenerics.R

@@ -67,3 +67,7 @@ setGeneric("getMetaAutocorrelation", function(object, ...) {
 setGeneric("getMetaDifferential", function(object, ...) {
     standardGeneric("getMetaDifferential")
 })
+
+setGeneric("hasProteinData", function(object, ...) {
+    standardGeneric("hasProteinData")
+})