Merge pull request #295 from MarioniLab/devel

Add NB-GLMM to master branch and upgrade to version 2.0

.github/workflows/RCMD_check.yml

@@ -6,14 +6,12 @@ on:
       - main
       - master
       - devel
-      - alice_fast
-      - alice
+      - genetic_case
   pull_request:
     branches:
       - main
       - master
       - devel
-      - alice
 
 name: R-CMD-check
 
@@ -42,11 +40,11 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -74,8 +72,8 @@ jobs:
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          BiocManager::install("MouseGastrulationData")
+          remotes::install_cran(c("rcmdcheck", "XML", "RCurl"))
+          BiocManager::install(c("MouseGastrulationData", "MouseThymusAgeing", "scRNAseq"))
         shell: Rscript {0}
 
       - name: Check

.gitignore

@@ -9,4 +9,6 @@ doc
 Meta
 docs
 .Rproj.user
-*yml
+*yml
+*.o
+*~

DESCRIPTION

@@ -1,31 +1,36 @@
 Package: miloR
 Type: Package
 Title: Differential neighbourhood abundance testing on a graph
-Version: 1.9.99
+Version: 1.99.9
 Authors@R:
-    c(person("Mike", "Morgan", role=c("aut", "cre"), email="[email protected]"),
-    comment=c(ORCID="0000-0003-0757-0711"),
+    c(person("Mike", "Morgan", role=c("aut", "cre"), email="[email protected]",
+     comment=c(ORCID="0000-0003-0757-0711")),
     person("Emma", "Dann", role=c("aut", "ctb"), email="[email protected]"))
 Description: Milo performs single-cell differential abundance testing. Cell states are modelled 
-    as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using a 
-    negative bionomial generalized linear model.
+    as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using either 
+    a negative bionomial generalized linear model or negative binomial generalized linear mixed model.
 License: GPL-3 + file LICENSE
 Encoding: UTF-8
 URL: https://marionilab.github.io/miloR
 BugReports: https://github.com/MarioniLab/miloR/issues
 biocViews: SingleCell, MultipleComparison, FunctionalGenomics, Software
+LinkingTo: Rcpp,
+           RcppArmadillo,
+           RcppEigen
 Depends: R (>= 4.0.0),
          edgeR
 Imports: BiocNeighbors,
          BiocGenerics,
          SingleCellExperiment,
          Matrix (>= 1.3-0),
+         MatrixGenerics,
          S4Vectors,
          stats,
          stringr,
          methods,
          igraph,
          irlba,
+         utils,
          cowplot,
          BiocParallel,
          BiocSingular,
@@ -42,10 +47,11 @@ Imports: BiocNeighbors,
          ggrepel,
          ggbeeswarm,
          RColorBrewer,
-         grDevices
+         grDevices,
+         Rcpp,
+         numDeriv
 Suggests: 
     testthat,
-    MASS,
     mvtnorm,
     scater,
     scran,
@@ -59,7 +65,9 @@ Suggests:
     MouseThymusAgeing,
     magick,
     RCurl,
+    MASS,
     curl,
+    scRNAseq,
     graphics
 RoxygenNote: 7.2.3
 NeedsCompilation: no
@@ -71,15 +79,19 @@ Collate:
     'buildGraph.R'
     'calcNhoodExpression.R'
     'calcNhoodDistance.R'
+    'checkSeparation.R'
     'countCells.R'
     'findNhoodMarkers.R'
     'graphSpatialFDR.R'
+    'glmm.R'
     'makeNhoods.R'
     'milo.R'
     'miloR-package.R'
     'methods.R'
     'plotNhoods.R'
     'sim_discrete.R'
+    'sim_family.R'
+    'sim_nbglmm.R'
     'sim_trajectory.R'
     'testNhoods.R'
     'testDiffExp.R'
@@ -88,4 +100,6 @@ Collate:
     'annotateNhoods.R'
     'groupNhoods.R'
     'findNhoodGroupMarkers.R'
+    'RcppExports.R'
+    'miloR.R'
 VignetteBuilder: knitr

NAMESPACE

@@ -10,20 +10,30 @@ export("nhoodIndex<-")
 export("nhoodReducedDim<-")
 export("nhoods<-")
 export(.calc_distance)
+export(.parse_formula)
+export(.rEParse)
 export(Milo)
+export(Satterthwaite_df)
 export(annotateNhoods)
 export(buildFromAdjacency)
 export(buildGraph)
 export(buildNhoodGraph)
 export(calcNhoodDistance)
 export(calcNhoodExpression)
+export(checkSeparation)
+export(computePvalue)
 export(countCells)
 export(findNhoodGroupMarkers)
 export(findNhoodMarkers)
+export(fitGLMM)
+export(glmmControl.defaults)
 export(graph)
 export(graphSpatialFDR)
 export(groupNhoods)
+export(initialiseG)
+export(initializeFullZ)
 export(makeNhoods)
+export(matrix.trace)
 export(nhoodAdjacency)
 export(nhoodCounts)
 export(nhoodDistances)
@@ -80,18 +90,26 @@ importFrom(BiocGenerics,which)
 importFrom(BiocNeighbors,KmknnParam)
 importFrom(BiocNeighbors,findKNN)
 importFrom(BiocParallel,SerialParam)
+importFrom(BiocParallel,bplapply)
+importFrom(BiocParallel,bpok)
+importFrom(BiocParallel,bpoptions)
+importFrom(BiocParallel,bptry)
 importFrom(BiocSingular,bsparam)
 importFrom(Matrix,Matrix)
 importFrom(Matrix,colSums)
 importFrom(Matrix,crossprod)
+importFrom(Matrix,diag)
 importFrom(Matrix,rowMeans)
 importFrom(Matrix,rowSums)
+importFrom(Matrix,solve)
 importFrom(Matrix,sparseMatrix)
 importFrom(Matrix,t)
 importFrom(Matrix,tcrossprod)
 importFrom(Matrix,tril)
 importFrom(Matrix,which)
+importFrom(MatrixGenerics,colSums2)
 importFrom(RColorBrewer,brewer.pal)
+importFrom(Rcpp,evalCpp)
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,SimpleList)
 importFrom(S4Vectors,coolcat)
@@ -158,6 +176,7 @@ importFrom(matrixStats,colMedians)
 importFrom(methods,as)
 importFrom(methods,callNextMethod)
 importFrom(methods,slot)
+importFrom(numDeriv,jacobian)
 importFrom(stats,as.formula)
 importFrom(stats,dist)
 importFrom(stats,hclust)
@@ -167,8 +186,15 @@ importFrom(stats,na.exclude)
 importFrom(stats,na.fail)
 importFrom(stats,na.omit)
 importFrom(stats,na.pass)
+importFrom(stats,pt)
+importFrom(stats,runif)
 importFrom(stats,setNames)
+importFrom(stats,var)
 importFrom(stringr,str_replace)
 importFrom(tibble,has_rownames)
 importFrom(tibble,rownames_to_column)
 importFrom(tidyr,pivot_longer)
+importFrom(utils,tail)
+importMethodsFrom(Matrix,"%*%")
+importMethodsFrom(Matrix,t)
+useDynLib(miloR)

NEWS.md

@@ -1,4 +1,10 @@
-# 1.5.0 (TBD)
+# 1.7.1 (2023-02-15)
++ Patch to fix `NA` plotting in `plotDABeeswarm`
+
+# 1.60 (2022-11-02)
++ Vignette describing the use of contrasts in `testNhoods`
+
+# 1.5.0 (2022-04-27)
 + Introduce plotting function to visualise neighbourhood count distributions for nhoods interest: `plotNhoodCounts`. Implemented by Nick Hirschmüller
 
 # 1.3.1 (2022-01-07)

R/AllClasses.R

@@ -1,4 +1,8 @@
-#' The Milo container class
+#' @title
+#' Milo class definition
+#'
+#' @description
+#' The class definition container to hold the data structures required for the Milo workflow.
 #'
 #' @slot graph An igraph object that represents the kNN graph
 #' @slot nhoods A CxN binary sparse matrix mapping cells to the neighbourhoods they belong to
@@ -14,14 +18,17 @@
 #' @slot nhoodGraph an igraph object that represents the graph of neighbourhoods
 #' @slot .k A hidden slot that stores the value of k used for graph building
 #'
+#' @returns A Milo class object - see object builder help pages for details
+#'
 #' @importClassesFrom Matrix dgCMatrix dsCMatrix dgTMatrix dgeMatrix ddiMatrix sparseMatrix
 setClassUnion("matrixORMatrix", c("matrix", "dgCMatrix", "dsCMatrix", "ddiMatrix",
-                                  "dgTMatrix", "dgeMatrix")) # is there a record for how long a virtual class can be?!
+                                  "dgTMatrix", "dgeMatrix"))
 setClassUnion("characterORNULL", c("character", "NULL"))
 setClassUnion("listORNULL", c("list", "NULL"))
 setClassUnion("numericORNULL", c("numeric", "NULL"))
 #' @aliases Milo
 #' @rdname Milo
+#'
 #' @export
 #' @importFrom SingleCellExperiment SingleCellExperiment
 #' @importFrom S4Vectors SimpleList