Add support for scGraph metric

Presented in Wang H. et al., Metric Mirages in Cell Embeddings, bioRxiv 2024.04.02.587824; doi: https://doi.org/10.1101/2024.04.02.587824
Original implementation: https://github.com/Genentech/Islander/blob/4fbf0d9336d4a3bb4667fec9aeb3bff551321622/src/scGraph.py

Author: fspecque

DESCRIPTION

@@ -50,7 +50,9 @@ Imports:
     parallelly,
     methods,
     scales,
-    cli
+    cli,
+    pbapply,
+    matrixStats
 Suggests: 
     SeuratData,
     lisi,
@@ -89,6 +91,7 @@ Collate:
     'metrics_kbet.R'
     'metrics_lisi.R'
     'metrics_nmi.R'
+    'metrics_scGraph.R'
     'metrics_silhouette.R'
     'scANVI.R'
     'scVI.R'

NAMESPACE

@@ -38,6 +38,7 @@ export(AddScoreLISI)
 export(AddScoreNMI)
 export(AddScoreRegressPC)
 export(AddScoreRegressPC.CellCycle)
+export(AddScoreScGraph)
 export(CellCycleScoringPerBatch)
 export(CombatIntegration)
 export(CondaEnv)
@@ -70,6 +71,7 @@ export(ScoreLISI)
 export(ScoreNMI)
 export(ScoreRegressPC)
 export(ScoreRegressPC.CellCycle)
+export(ScoreScGraph)
 export(SymmetrizeKnn)
 export(UpdateEnvCache)
 export(bbknnIntegration)
@@ -121,11 +123,14 @@ importFrom(Seurat,CreateSeuratObject)
 importFrom(Seurat,DefaultAssay)
 importFrom(Seurat,FindClusters)
 importFrom(Seurat,FindNeighbors)
+importFrom(Seurat,FindVariableFeatures)
 importFrom(Seurat,LogSeuratCommand)
 importFrom(Seurat,RunPCA)
+importFrom(Seurat,ScaleData)
 importFrom(Seurat,SelectIntegrationFeatures)
 importFrom(Seurat,SelectIntegrationFeatures5)
 importFrom(Seurat,SelectSCTIntegrationFeatures)
+importFrom(Seurat,SplitObject)
 importFrom(Seurat,VariableFeatures)
 importFrom(Seurat,as.SingleCellExperiment)
 importFrom(SeuratObject,"%iff%")
@@ -144,6 +149,7 @@ importFrom(SeuratObject,Features)
 importFrom(SeuratObject,GetAssayData)
 importFrom(SeuratObject,Graphs)
 importFrom(SeuratObject,JoinLayers)
+importFrom(SeuratObject,Key)
 importFrom(SeuratObject,LayerData)
 importFrom(SeuratObject,Layers)
 importFrom(SeuratObject,LogSeuratCommand)
@@ -184,6 +190,7 @@ importFrom(dplyr,case_when)
 importFrom(dplyr,count)
 importFrom(dplyr,cur_column)
 importFrom(dplyr,desc)
+importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,group_map)
@@ -197,6 +204,7 @@ importFrom(dplyr,pull)
 importFrom(dplyr,rename)
 importFrom(dplyr,rowwise)
 importFrom(dplyr,select)
+importFrom(dplyr,starts_with)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)
@@ -243,6 +251,7 @@ importFrom(harmony,harmony_options)
 importFrom(igraph,components)
 importFrom(igraph,distances)
 importFrom(igraph,graph_from_adjacency_matrix)
+importFrom(matrixStats,rowMaxs)
 importFrom(methods,"slot<-")
 importFrom(methods,as)
 importFrom(methods,callNextMethod)
@@ -253,6 +262,9 @@ importFrom(methods,slotNames)
 importFrom(methods,validObject)
 importFrom(parallel,mcmapply)
 importFrom(parallelly,supportsMulticore)
+importFrom(pbapply,pblapply)
+importFrom(pbapply,pbmapply)
+importFrom(pbapply,pbsapply)
 importFrom(purrr,imap)
 importFrom(purrr,map2)
 importFrom(purrr,reduce)
@@ -300,6 +312,7 @@ importFrom(stats,bw.bcv)
 importFrom(stats,bw.nrd)
 importFrom(stats,bw.nrd0)
 importFrom(stats,bw.ucv)
+importFrom(stats,cor)
 importFrom(stats,density)
 importFrom(stats,lm)
 importFrom(stats,median)
@@ -311,6 +324,7 @@ importFrom(sva,ComBat)
 importFrom(sva,ComBat_seq)
 importFrom(tibble,add_column)
 importFrom(tibble,add_row)
+importFrom(tibble,column_to_rownames)
 importFrom(tibble,rownames_to_column)
 importFrom(tibble,tibble)
 importFrom(tidyr,pivot_longer)

NEWS.md

@@ -1,5 +1,8 @@
 # SeuratIntegrate (development version)
 
+* Add support for scGraph metric (https://doi.org/10.1101/2024.04.02.587824)
+
+
 # SeuratIntegrate 0.4.0
 
 * Initial public release

R/globals.R

@@ -6,4 +6,5 @@ if (getRversion() >= "2.15.1")
                     "method", "var", "H", "proba", "sigmas", "rhos",
                     "rows", "cols", "vals", "distances",
                     "Integration", "Overall.score", "Score", "y", "Score.type",
-                    "RECT_x", "RECT_y", "sub.object", "df.score"))
+                    "RECT_x", "RECT_y", "sub.object", "df.score",
+                    "celltype", "cells_keep", "batches_keep"))