Merge pull request #1499 from GreenleafLab/release_1.0.2

Release 1.0.2

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: ArchR
 Type: Package
-Date: 2020-11-23
+Date: 2022-04-03
 Title: Analyzing single-cell regulatory chromatin in R.
-Version: 1.0.1
+Version: 1.0.2
 Authors@R: c(
     person("Jeffrey", "Granja", email = "jgranja.stanford@gmail.com", role = c("aut","cre")),
     person("Ryan", "Corces", role = "aut"))
@@ -11,9 +11,17 @@ Roxygen: list(markdown = TRUE)
 License: GPL (>= 2)
 LinkingTo: Rcpp
 LazyData: TRUE
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Encoding: UTF-8
 Imports:
+    ggplot2,
+    SummarizedExperiment,
+    data.table,
+    Matrix,
+    rhdf5,
+    magrittr,
+    S4Vectors (>= 0.9.25),
+    BiocGenerics,
     Rcpp (>= 0.12.16),
     matrixStats,
     plyr,
@@ -29,17 +37,9 @@ Imports:
     grid,
     gridExtra,
     Biostrings,
-    ComplexHeatmap
-Depends:
-    ggplot2,
-    SummarizedExperiment,
-    data.table,
-    Matrix,
-    rhdf5,
-    magrittr,
-    S4Vectors (>= 0.9.25),
-    BiocGenerics,
+    ComplexHeatmap,
     GenomicRanges
+Depends:
 Collate: 
     'AllClasses.R'
     'AnnotationGenome.R'

NAMESPACE

@@ -3,10 +3,10 @@
 S3method("$",ArchRProject)
 S3method("$<-",ArchRProject)
 S3method("[",ArchRProject)
-S3method(.DollarNames,ArchRProject)
 export("%bcin%")
 export("%bcni%")
 export("%ni%")
+export(.DollarNames.ArchRProject)
 export(ArchRBrowser)
 export(ArchRBrowserTrack)
 export(ArchRPalettes)
@@ -158,5 +158,7 @@ export(subsetCells)
 export(theme_ArchR)
 export(trajectoryHeatmap)
 export(validBSgenome)
+import(data.table)
+importFrom(GenomicRanges,GRanges)
 importFrom(Rcpp,sourceCpp)
 useDynLib(ArchR)

R/AllClasses.R

@@ -1,5 +1,7 @@
 #' @useDynLib ArchR
 #' @importFrom Rcpp sourceCpp
+#' @importFrom GenomicRanges GRanges
+#' @import data.table
 NULL
 
 setClassUnion("characterOrNull", c("character", "NULL"))
@@ -569,51 +571,29 @@ saveArchRProject <- function(
       newProj@imputeWeights <- SimpleList()
     }
 
-    #Copy Other Folders 2 layers nested
+    #Copy Recursively
     message("Copying Other Files...")
     for(i in seq_along(oldFiles)){
-
-      fin <- file.path(outDirOld, oldFiles[i])
-      fout <- file.path(outputDirectory, oldFiles[i])
-      message(sprintf("Copying Other Files (%s of %s): %s", i, length(oldFiles), basename(fin)))
-
-      if(dir.exists(fin)){
-
-        dir.create(file.path(outputDirectory, basename(fin)), showWarnings=FALSE)
-        fin2 <- list.files(fin, full.names = TRUE)
-
-        for(j in seq_along(fin2)){
-
-          if(dir.exists(fin2[j])){
-
-            dir.create(file.path(outputDirectory, basename(fin), basename(fin2)[j]), showWarnings=FALSE)
-            fin3 <- list.files(fin2[j], full.names = TRUE)
-
-            for(k in seq_along(fin3)){
-
-              cf <- file.copy(fin3[k], file.path(fout, basename(fin3[k])), overwrite = overwrite)
-
-            }
-
-          }else{
-
-            cf <- file.copy(fin2[j], file.path(fout, basename(fin2[j])), overwrite = overwrite)
-
-          }
-
-        }
-
-      }else{
-
-        cf <- file.copy(fin, fout, overwrite = overwrite)
-
-      }
-
+      message(sprintf("Copying Other Files (%s of %s): %s", i, length(oldFiles), oldFiles[i]))
+      oldPath <- file.path(outDirOld, oldFiles[i])
+      file.copy(oldPath, outputDirectory, recursive=TRUE, overwrite=overwrite)
     }
 
+    #Set New Info
     newProj@sampleColData <- newProj@sampleColData[names(ArrowFilesNew), , drop = FALSE]
     newProj@sampleColData$ArrowFiles <- ArrowFilesNew[rownames(newProj@sampleColData)]
 
+    #Check for Group Coverages Copied
+    groupC <- length(newProj@projectMetadata$GroupCoverages)
+    if(length(groupC) > 0){
+      for(z in seq_len(groupC)){
+        zdata <- newProj@projectMetadata$GroupCoverages[[z]]$coverageMetadata
+        zfiles <- gsub(outDirOld, outputDirectory, zdata$File)
+        newProj@projectMetadata$GroupCoverages[[z]]$coverageMetadata$File <- zfiles
+        stopifnot(all(file.exists(zfiles)))
+      }
+    }
+
   }
 
   message("Saving ArchRProject...")

R/AnnotationGenome.R

@@ -6,9 +6,10 @@
 #' @param chromSizes A `GRanges` object containing chromosome start and end coordinates.
 #' @param blacklist A `GRanges` object containing regions that should be excluded from analyses due to unwanted biases.
 #' @param filter A boolean value indicating whether non-standard chromosome scaffolds should be excluded.
-#' These "non-standard" chromosomes are defined by `filterChrGR()`.
+#' These "non-standard" chromosomes are defined by `filterChrGR()` and by manual annotation using the `filterChr` parameter.
 #' @param filterChr A character vector indicating the seqlevels that should be removed if manual removal is desired for certain seqlevels.
-#' If no manual removal is desired, `filterChr` should be set to `NULL`.
+#' If no manual removal is desired, `filterChr` should be set to `NULL`. If `filter` is set to `TRUE` but `filterChr` is set to `NULL`,
+#' non-standard chromosomes will still be removed as defined in `filterChrGR()`.
 #' @export
 createGenomeAnnotation <- function(
   genome = NULL,
@@ -24,23 +25,27 @@ createGenomeAnnotation <- function(
   .validInput(input = filter, name = "filter", valid = c("boolean"))
   .validInput(input = filterChr, name = "filterChr", valid = c("character", "null"))
 
-  if(is.null(genome) | is.null(blacklist) | is.null(chromSizes)){
+  ##################
+  message("Getting genome..")
+  #validBSgenome works on both character and BSgenome inputs, which are the only allowable inputs to the param
+  bsg <- validBSgenome(genome)
+  genome <- bsg@pkgname
 
-    ##################
-    message("Getting genome..")
-    bsg <- validBSgenome(genome)
-    genome <- bsg@pkgname
-
-    ##################
-    message("Getting chromSizes..")
+  if(is.null(chromSizes)) {
+    message("Attempting to infer chromSizes..")
     chromSizes <- GRanges(names(seqlengths(bsg)), IRanges(1, seqlengths(bsg)))
     if(filter){
-        chromSizes <- filterChrGR(chromSizes, remove = filterChr)
+      chromSizes <- filterChrGR(chromSizes, remove = filterChr)
     }
     seqlengths(chromSizes) <- end(chromSizes)
+  } else {
+    message("Using provided chromSizes..")
+    chromSizes <- .validGRanges(chromSizes)
+  }
 
+  if(is.null(blacklist)){
     ##################
-    message("Getting blacklist..")
+    message("Attempting to infer blacklist..")
 
     genomeName <- tryCatch({
       bsg@provider_version
@@ -50,15 +55,9 @@ createGenomeAnnotation <- function(
 
     blacklist <- .getBlacklist(genome = genomeName)
 
-  }else{
-
-    bsg <- validBSgenome(genome)
-    genome <- bsg@pkgname
-
-    chromSizes <- .validGRanges(chromSizes)
-
+  } else {
+    message("Using provided blacklist...")
     blacklist <- .validGRanges(blacklist)
-
   }
 
   SimpleList(genome = genome, chromSizes = chromSizes, blacklist = blacklist)
@@ -172,7 +171,7 @@ createGeneAnnotation <- function(
 
     ###########################
     message("Getting TSS..")
-    TSS <- unique(resize(GenomicFeatures::transcripts(TxDb), width = 1, fix = "start"))
+    TSS <- unique(GenomicRanges::resize(GenomicFeatures::transcripts(TxDb), width = 1, fix = "start"))
 
     if(!is.null(inGenes)){
       genes <- .validGRanges(inGenes)