merge dev and master

drieslab · Oct 10, 2020 · 627dbf0 · 627dbf0
2 parents f8b6d5b + 8be522d
commit 627dbf0
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -11,3 +11,4 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+.Rbuildignore.save
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,39 +1,41 @@
 Package: Giotto
 Title: Spatial single-cell transcriptomics toolbox
-Version: 0.3.6.9000
+Version: 0.3.6.9058
 Authors@R: c(
 	person("Ruben", "Dries", email = "[email protected]",
 		 role = c("aut", "cre")),
-	person("Huipeng", "Li", email = "[email protected]",
-		role = c("aut")),
 	person("Qian", "Zhu", email = "[email protected]",
 		 role = c("aut")),
+	person("Huipeng", "Li", email = "[email protected]",
+		role = c("aut")),
 	person("Rui", "Dong", email = "[email protected]",
 		 role = c("aut")),
 	person("Guo-Cheng", "Yuan", email = "[email protected]",
 		 role = c("aut"))
 	)
-Description: Toolbox to process, analyze and visualize spatial single-cell expression data
+Description: Toolbox to process, analyze and visualize spatial single-cell expression data.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 URL: https://rubd.github.io/Giotto/, https://github.com/RubD/Giotto
 BugReports: https://github.com/RubD/Giotto/issues
 RoxygenNote: 7.1.1
 Depends:
-    base (>= 3.5.1),
-    utils (>= 3.5.1),
-    R (>= 3.5.1)
+    base (>= 3.5.0),
+    utils (>= 3.5.0),
+    R (>= 3.5.0)
 Imports:
     data.table (>= 1.12.2),
     deldir,
+    dendextend (>= 1.13.0),
     ggplot2 (>= 3.1.1),
     Matrix,
     magick,
     matrixStats (>= 0.55.0),
     methods,
     uwot (>= 0.0.0.9010),
     cowplot (>= 0.9.4),
+    ClusterR,
     grDevices,
     graphics,
     RColorBrewer (>= 1.1-2),
@@ -61,19 +63,30 @@ Imports:
     Rtsne (>= 0.15),
     rlang (>= 0.4.3),
     R.utils,
-    fitdistrplus,
+    fitdistrplus
 Suggests:
+    Biobase,
+    biomaRt,
+    circlize,
+    FactoMineR,
+    factoextra,
+    geometry,
+    ggforce,
+    ggrepel,
+    htmlwidgets,
+    jackstraw,
     knitr,
-    rmarkdown,
     MAST,
-    scran (>= 1.10.1),
+    multinet (>= 3.0.2),
     png,
-    FactoMineR,
+    quadprog,
+    rmarkdown,
+    RTriangle (>= 1.6-0.10),
+    scran (>= 1.10.1),
+    SingleCellExperiment,
+    SPARK,
     tiff,
-    biomaRt,
-    trendsceek,
-    multinet (>= 3.0.2),
-    RTriangle (>= 1.6-0.10)
+    trendsceek
 biocViews:
 VignetteBuilder: knitr
 LinkingTo: 

diff --git a/Giotto_0.3.5.pdf b/Giotto_0.3.5.pdf
diff --git a/Giotto_0.3.6.9000.pdf b/Giotto_0.3.6.9000.pdf
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,7 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
-export(FSV_show)
 export(PAGEEnrich)
 export(addCellIntMetadata)
 export(addCellMetadata)
@@ -15,11 +14,13 @@ export(addHMRF)
 export(addNetworkLayout)
 export(addStatistics)
 export(adjustGiottoMatrix)
-export(all_plots_save_function)
+export(anndataToGiotto)
 export(annotateGiotto)
 export(annotateSpatialGrid)
 export(annotateSpatialNetwork)
 export(binSpect)
+export(binSpectMulti)
+export(binSpectSingle)
 export(calculateHVG)
 export(calculateMetaTable)
 export(calculateMetaTableCells)
@@ -31,16 +32,18 @@ export(cellProximitySpatPlot)
 export(cellProximitySpatPlot2D)
 export(cellProximitySpatPlot3D)
 export(cellProximityVisPlot)
-export(cellProximityVisPlot_2D_ggplot)
-export(cellProximityVisPlot_2D_plotly)
-export(cellProximityVisPlot_3D_plotly)
 export(changeGiottoInstructions)
 export(changeImageBg)
+export(checkGiottoEnvironment)
 export(clusterCells)
 export(clusterSpatialCorGenes)
+export(colMeans_giotto)
+export(colSums_giotto)
 export(combCCcom)
 export(combineCPG)
 export(combineCellProximityGenes)
+export(combineICG)
+export(combineInteractionChangedGenes)
 export(combineMetadata)
 export(convertEnsemblToGeneSymbol)
 export(createCrossSection)
@@ -50,6 +53,7 @@ export(createGiottoObject)
 export(createGiottoVisiumObject)
 export(createMetagenes)
 export(createNearestNetwork)
+export(createSpatialDefaultGrid)
 export(createSpatialDelaunayNetwork)
 export(createSpatialEnrich)
 export(createSpatialGrid)
@@ -75,27 +79,26 @@ export(doKmeans)
 export(doLeidenCluster)
 export(doLeidenSubCluster)
 export(doLouvainCluster)
-export(doLouvainCluster_community)
-export(doLouvainCluster_multinet)
 export(doLouvainSubCluster)
-export(doLouvainSubCluster_community)
-export(doLouvainSubCluster_multinet)
 export(doRandomWalkCluster)
 export(doSNNCluster)
 export(estimateImageBg)
 export(exportGiottoViewer)
 export(exprCellCellcom)
-export(extractNearestNetwork)
 export(fDataDT)
 export(filterCPG)
 export(filterCellProximityGenes)
 export(filterCombinations)
 export(filterDistributions)
 export(filterGiotto)
+export(filterICG)
+export(filterInteractionChangedGenes)
 export(findCPG)
 export(findCellProximityGenes)
 export(findGiniMarkers)
 export(findGiniMarkers_one_vs_all)
+export(findICG)
+export(findInteractionChangedGenes)
 export(findMarkers)
 export(findMarkers_one_vs_all)
 export(findMastMarkers)
@@ -108,14 +111,17 @@ export(getClusterSimilarity)
 export(getDendrogramSplits)
 export(getDistinctColors)
 export(getGiottoImage)
+export(getSpatialDataset)
 export(heatmSpatialCorGenes)
 export(hyperGeometricEnrich)
 export(insertCrossSectionGenePlot3D)
 export(insertCrossSectionSpatPlot3D)
+export(installGiottoEnvironment)
 export(jackstrawPlot)
 export(loadHMRF)
 export(makeSignMatrixPAGE)
 export(makeSignMatrixRank)
+export(mean_giotto)
 export(mergeClusters)
 export(normalizeGiotto)
 export(pDataDT)
@@ -127,6 +133,8 @@ export(plotCombineCCcom)
 export(plotCombineCPG)
 export(plotCombineCellCellCommunication)
 export(plotCombineCellProximityGenes)
+export(plotCombineICG)
+export(plotCombineInteractionChangedGenes)
 export(plotGiottoImage)
 export(plotHeatmap)
 export(plotICG)
@@ -146,19 +154,25 @@ export(plotUMAP)
 export(plotUMAP_2D)
 export(plotUMAP_3D)
 export(plot_spat_voronoi_layer_ggplot)
-export(plotly_axis_scale_2D)
-export(plotly_axis_scale_3D)
-export(plotly_grid)
-export(plotly_network)
-export(print.giotto)
 export(rankEnrich)
 export(rankSpatialCorGroups)
 export(readExprMatrix)
 export(readGiottoInstructions)
 export(removeCellAnnotation)
 export(removeGeneAnnotation)
+export(removeGiottoEnvironment)
 export(replaceGiottoInstructions)
+export(rowMeans_giotto)
+export(rowSums_giotto)
+export(runDWLSDeconv)
+export(runHyperGeometricEnrich)
+export(runPAGEEnrich)
+export(runPAGEEnrich_OLD)
 export(runPCA)
+export(runPatternSimulation)
+export(runRankEnrich)
+export(runSpatialDeconv)
+export(runSpatialEnrich)
 export(runUMAP)
 export(runtSNE)
 export(screePlot)
@@ -178,6 +192,9 @@ export(showSaveParameters)
 export(showSpatialCorGenes)
 export(signPCA)
 export(silhouetteRank)
+export(silhouetteRankTest)
+export(simulateOneGenePatternGiottoObject)
+export(spark)
 export(spatCellCellcom)
 export(spatCellPlot)
 export(spatCellPlot2D)
@@ -206,39 +223,19 @@ export(stitchTileCoordinates)
 export(subClusterCells)
 export(subsetGiotto)
 export(subsetGiottoLocs)
+export(t_giotto)
 export(trendSceek)
 export(updateGiottoImage)
 export(viewHMRFresults)
 export(viewHMRFresults2D)
 export(viewHMRFresults3D)
 export(violinPlot)
-export(visDimGenePlot)
-export(visDimGenePlot_2D_ggplot)
-export(visDimGenePlot_3D_plotly)
-export(visDimPlot)
-export(visDimPlot_2D_ggplot)
-export(visDimPlot_2D_plotly)
-export(visDimPlot_3D_plotly)
-export(visForceLayoutPlot)
-export(visGenePlot)
-export(visGenePlot_2D_ggplot)
-export(visGenePlot_3D_plotly)
-export(visPlot)
-export(visPlot_2D_ggplot)
-export(visPlot_2D_plotly)
-export(visPlot_3D_plotly)
-export(visSpatDimGenePlot)
-export(visSpatDimGenePlot_2D)
-export(visSpatDimGenePlot_3D)
-export(visSpatDimPlot)
-export(visSpatDimPlot_2D)
-export(visSpatDimPlot_3D)
 export(writeHMRFresults)
 exportClasses(giotto)
-exportMethods(show)
 import(data.table)
 import(ggplot2)
 import(utils)
 importFrom(Rcpp,sourceCpp)
 importFrom(magrittr,"%>%")
+importFrom(methods,new)
 useDynLib(Giotto)
diff --git a/R/NN_network.R b/R/NN_network.R
@@ -51,7 +51,12 @@
 #'
 #' @export
 #' @examples
-#'     createNearestNetwork(gobject)
+#'
+#' data(mini_giotto_single_cell)
+#'
+#' mini_giotto_single_cell <- createNearestNetwork(gobject = mini_giotto_single_cell,
+#'                                                 dimensions_to_use = 1:3, k = 3)
+#'
 createNearestNetwork <- function(gobject,
                                  type = c('sNN', 'kNN'),
                                  dim_reduction_to_use = 'pca',
@@ -211,8 +216,6 @@ createNearestNetwork <- function(gobject,
 #' Currently only the force-directed graph layout "drl", see \code{\link[igraph]{layout_with_drl}},
 #' is implemented. This provides an alternative to tSNE or UMAP based visualizations.
 #' @export
-#' @examples
-#'     addNetworkLayout(gobject)
 addNetworkLayout = function(gobject,
                             nn_network_to_use = "sNN",
                             network_name = "sNN.pca",
@@ -273,9 +276,13 @@ addNetworkLayout = function(gobject,
 #' @name nnDT_to_kNN
 #' @description Convert a nearest network data.table to a kNN object
 #' @param nnDT nearest neighbor network in data.table format
+#' @keywords internal
 #' @return kNN object
 nnDT_to_kNN <- function(nnDT) {
 
+  # data.table variable
+  from = NULL
+
   k = unique(table(nnDT$from))
 
   if(length(k) > 1) {
@@ -300,18 +307,16 @@ nnDT_to_kNN <- function(nnDT) {
 
 
 
-#' @title extractNearestNetwork
-#' @name extractNearestNetwork
+#' @title select_NearestNetwork
+#' @name select_NearestNetwork
 #' @description Extracts a NN-network from a Giotto object
 #' @param gobject giotto object
 #' @param nn_network_to_use kNN or sNN
 #' @param network_name name of NN network to be used
 #' @param output return a igraph or data.table object
 #' @return igraph or data.table object
-#' @export
-#' @examples
-#'     extractNearestNetwork(gobject)
-extractNearestNetwork = function(gobject,
+#' @keywords internal
+select_NearestNetwork = function(gobject,
                                  nn_network_to_use = 'sNN',
                                  network_name = 'sNN.pca',
                                  output = c('igraph', 'data.table')) {
@@ -340,3 +345,21 @@ extractNearestNetwork = function(gobject,
 
 }
 
+
+#' @title extractNearestNetwork
+#' @name extractNearestNetwork
+#' @description Function to calculate gene signature enrichment scores per spatial position using a rank based approach.
+#' @inheritDotParams select_NearestNetwork
+#' @seealso \code{\link{select_NearestNetwork}}
+#' @keywords internal
+extractNearestNetwork = function(...) {
+
+  .Deprecated(new = "select_NearestNetwork")
+
+  select_NearestNetwork(...)
+
+}
+
+
+
+