Merge branch 'dev'

.circleci/config.yml

@@ -1,4 +1,4 @@
-version: 2
+version: 3
 jobs:
   build:
     docker:
@@ -12,23 +12,23 @@ jobs:
           command: sudo apt-get update -y && sudo apt-get install tk zip libcurl4-openssl-dev libssl-dev libxml2-dev libgmp-dev libglpk-dev -y  
       - run: 
           name: Install matrixStats
-          command: R -e "install.packages('https://cran.r-project.org/src/contrib/matrixStats_0.61.0.tar.gz', repos=NULL, type='source')"
+          command: R -e "install.packages('https://cran.r-project.org/src/contrib/matrixStats_1.2.0.tar.gz', repos=NULL, type='source')"
       - run: 
           name: Install DESeq2, SummarizedExperiment
           command:  R -e "BiocManager::install(c('DESeq2', 'SummarizedExperiment'), ask = FALSE, update = TRUE)"       
       - run:
           name: Install package dependencies
           command: R -e "devtools::install_deps(dep = TRUE)" 
       - run: 
-          name: Install sccore v1.0.2
+          name: Install sccore v1.0.4
           command: R -e "install.packages('pbmcapply')" \
-                   R -e "install.packages('https://cran.r-project.org/src/contrib/sccore_1.0.2.tar.gz', repos=NULL, type='source')" \
+                   R -e "install.packages('https://cran.r-project.org/src/contrib/sccore_1.0.4.tar.gz', repos=NULL, type='source')" \
       - run: 
-          name: Install igraph v1.2.10
-          command: R -e "install.packages('https://cran.r-project.org/src/contrib/igraph_1.2.10.tar.gz', repos=NULL, type='source')"   
+          name: Install igraph v1.6.0
+          command: R -e "install.packages('https://cran.r-project.org/src/contrib/igraph_1.6.0.tar.gz', repos=NULL, type='source')"   
       - run: 
-          name: Install leidenAlg v1.0.5
-          command: R -e "install.packages('https://cran.r-project.org/src/contrib/leidenAlg_1.0.5.tar.gz', repos=NULL, type='source')"
+          name: Install leidenAlg v1.1.2
+          command: R -e "install.packages('https://cran.r-project.org/src/contrib/leidenAlg_1.1.2.tar.gz', repos=NULL, type='source')"
       - run:
           name: Build package
           command: R CMD build .

CHANGELOG.md

@@ -1,19 +1,23 @@
 ## Upcoming
 
+## [1.5.1] - 2024-22-January
+- Remove C++11 flag
+- Fixed various roxygen2 typos and variable names for docs consistency
+- S3 method exports, buildWijMatrix.*
 
-## [1.5.0] - 2022-17-Oct
+## [1.5.0] - 2022-17-October
 - Fixed compilation issue on certain OS configurations
 
 
-## [1.4.9] - 2022-29-Sept
+## [1.4.9] - 2022-29-September
 - Fix multithreading with largeVis, GitHub issue #129
 
-## [1.4.8] - 2022-25-Sept
+## [1.4.8] - 2022-25-September
 - Add back velocityInfoConos()
 - Remove 'Matrix.utils' as dependency
 
 
-## [1.4.7] - 2022-04-Sept
+## [1.4.7] - 2022-04-September
 - Fixes for Matrix, updated versions 1.4.2, 1.5.0
 - Use `inherits()` for conditionals with class()
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: conos
 Title: Clustering on Network of Samples
-Version: 1.5.0
+Version: 1.5.1
 Authors@R: c(person("Viktor","Petukhov", email="[email protected]", role="aut"), person("Nikolas","Barkas", email="[email protected]", role="aut"), person("Peter", "Kharchenko", email = "[email protected]", role = "aut"), person("Weiliang", "Qiu", email = "[email protected]", role = c("ctb")), person("Evan", "Biederstedt", email="[email protected]", role=c("aut", "cre")))
 Description: Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
 License: GPL-3
@@ -33,7 +33,7 @@ Imports:
     stats,
     tools,
     utils
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Suggests:
     AnnotationDbi,
     BiocParallel,

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(buildWijMatrix,CsparseMatrix)
+S3method(buildWijMatrix,TsparseMatrix)
 export("edgeMat<-")
 export(Conos)
 export(basicSeuratProc)

R/conos.R

@@ -468,7 +468,7 @@ getClusterRelationshipConsistency <- function(p2list, pjc) {
 #' @param p2list list of pagoda2 object on which clustering was generated
 #' @param pjc the result of joint clustering
 #' @param pc.samples.cutoff numeric The percent of the number of the total samples that a cluster has to span to be considered global (default=0.9)
-#' @param min.cell.count.per.samples numeric The minimum number of cells of cluster in sample to be considered as represented in that sample (default=10)
+#' @param min.cell.count.per.sample numeric The minimum number of cells of cluster in sample to be considered as represented in that sample (default=10)
 #' @return percent of clusters that are global given the above criteria
 #' @keywords internal
 getPercentGlobalClusters <- function(p2list, pjc, pc.samples.cutoff = 0.9, min.cell.count.per.sample = 10) {

R/de_functions.R

@@ -546,7 +546,7 @@ getDifferentialGenesP2 <- function(p2.samples, groups, z.threshold=3.0, upregula
 
 #' Check that the count data contain only integer counts
 #'
-#' @param aggregated.samples the count data from aggreaged samples input to DESeq
+#' @param input.matrix the count data from aggregated samples input to DESeq
 #' @return if non-integer counts are found, an error is returned
 #' @keywords internal
 checkCountsWholeNumbers <- function(input.matrix){

R/largeVis.R

@@ -19,12 +19,14 @@ NULL
 buildWijMatrix <- function(x, threads=NULL, perplexity=50) UseMethod("buildWijMatrix")
 
 #' @rdname buildWijMatrix
+#' @export
 buildWijMatrix.TsparseMatrix <- function(x, threads = NULL, perplexity = 50) {
   wij <- referenceWij(x@j, x@i, x@x^2, as.integer(threads), perplexity)
   return(wij)
 }
 
 #' @rdname buildWijMatrix
+#' @export
 buildWijMatrix.CsparseMatrix <- function(x, threads = NULL, perplexity = 50) {
   is <- rep(0:(ncol(x) - 1), diff(x@p))
   wij <- referenceWij(is, x@i, x@x^2, as.integer(threads), perplexity)

R/plot.R

@@ -281,7 +281,7 @@ plotClusterBoxPlotsByAppType <- function(conos.obj, clustering=NULL, apptypes=NU
 #' @param conos.obj conos object
 #' @param clustering character Name of the clustering to use (default='multi level')
 #' @param min.samples.expressing numeric Minimum number of samples that must have the genes upregulated in the respective cluster (default=0)
-#' @param min.percent.samples.expression numeric Minumum percent of samples that must have the gene upregulated (default=0)
+#' @param min.percent.samples.expressing numeric Minumum percent of samples that must have the gene upregulated (default=0)
 #' @return List of consistent genes per each cluster
 #' @keywords internal
 getGlobalClusterMarkers <- function(conos.obj, clustering='multi level',

README.md

@@ -238,5 +238,5 @@ The R package can be cited as:
 ```
 Viktor Petukhov, Nikolas Barkas, Peter Kharchenko, and Evan
 Biederstedt (2021). conos: Clustering on Network of Samples. R
-package version 1.5.0.
+package version 1.5.1.
 ```

src/Makevars

@@ -1,3 +1,2 @@
 PKG_CXXFLAGS=-I"./include" $(SHLIB_OPENMP_CXXFLAGS) 
-PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lstdc++ -lm `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)
-CXX_STD = CXX11
+PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lstdc++ -lm `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS)

src/Makevars.win

@@ -1,3 +1,2 @@
 PKG_CXXFLAGS=-I"./include" $(SHLIB_OPENMP_CXXFLAGS) 
 PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lstdc++ -lm $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "Rcpp:::LdFlags()") $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) 
-CXX_STD = CXX11

src/RcppExports.cpp

@@ -2,7 +2,6 @@
 // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 #include <RcppArmadillo.h>
-#define NDEBUG 1
 #include <RcppEigen.h>
 #include <Rcpp.h>