Merge pull request #17 from compbiomed/devel

Devel
compbiomed · Oct 17, 2023 · 74391f2 · 74391f2
2 parents f290489 + 5a3df3d
commit 74391f2
Show file tree

Hide file tree

Showing 415 changed files with 3,463 additions and 7,305 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: singleCellTK
 Type: Package
 Title: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
-Version: 2.10.1
+Version: 2.11.0
 Authors@R: c(person(given="Yichen", family="Wang", email="wangych@bu.edu", role=c("aut", "cre"),
                     comment = c(ORCID = "0000-0003-4347-5199")),
              person(given="Irzam", family="Sarfraz", email="isarfraz@bu.edu", role=c("aut"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,9 +1,15 @@
 Changes in Version 2.10.1 (2023-07-26)
 ================================================================================
-* Added bubble plot
-* Added support for batch processing multiple inputs
-* Added support for importing and exporting AnnData objects
-* Fixed a bug causing YAML output files to be empty
+* Added function for bubble plot
+* In SCTK-QC pipeline, added support for batch processing multiple inputs
+* In SCTK-QC pipeline, added support for importing and exporting AnnData objects
+* In SCTK-QC pipeline, fixed a bug causing YAML output files to be empty
+* Update the SCTK-QC tutorial 
+* Fixed bug in combineSCE causing it to create multiple copies of row or column data
+
+Changes in Version 2.10.0 (2023-04-25)
+================================================================================
+* Updated version to match Bioconductor 3.17
 
 Changes in Version 2.8.1 (2023-03-10)
 ================================================================================

diff --git a/R/celda_decontX.R b/R/celda_decontX.R
@@ -151,8 +151,8 @@ runDecontX <- function(inSCE,
   }
 
 
-
-  message(paste0(date(), " ... Running 'DecontX'"))
+  p <- paste0(date(), " ... Running 'DecontX'")
+  message(p)
 
   ## keep a copy of original decontX result, if there's any
   oldColData <- NULL

diff --git a/R/data.R b/R/data.R
@@ -13,6 +13,7 @@
 #' @source DOI: 10.1126/science.aaa1934
 #' @keywords datasets
 #' @usage data("mouseBrainSubsetSCE")
+#' @return A subset of 30 cells from a single cell RNA-Seq experiment
 #' @examples
 #' data("mouseBrainSubsetSCE")
 "mouseBrainSubsetSCE"
@@ -33,6 +34,8 @@
 #' @format A \link[SingleCellExperiment]{SingleCellExperiment} object.
 #' @keywords datasets
 #' @usage data("scExample")
+#' @return Example Single Cell RNA-Seq data in SingleCellExperiment Object,
+#' subset of 10x public dataset
 #' @examples
 #' data("scExample")
 "sce"
@@ -47,6 +50,8 @@
 #' `'beta'`, that could be found in both original studies with relatively
 #' large population were kept for cleaner demonstration.
 #' @usage data('sceBatches')
+#' @return Example Single Cell RNA-Seq data in SingleCellExperiment object, with
+#' different batches annotated
 "sceBatches"
 
 #' Stably Expressed Gene (SEG) list obect, with SEG sets for human and mouse.
@@ -59,6 +64,7 @@
 #' @source \code{data('segList', package='scMerge')}
 #' @keywords datasets
 #' @usage data('SEG')
+#' @return Stably Expressed Gene (SEG) list obect, with SEG sets for human and mouse.
 #' @examples
 #' data('SEG')
 #' humanSEG <- SEG$human
@@ -77,6 +83,7 @@
 #' @format A data.frame.
 #' @keywords datasets
 #' @usage data("msigdb_table")
+#' @return A table of gene set categories
 #' @examples
 #' data("msigdb_table")
 "msigdb_table"
@@ -93,6 +100,7 @@
 #' @format A list
 #' @keywords datasets
 #' @usage data("MitoGenes")
+#' @return List of mitochondrial genes of multiple reference
 #' @examples
 #' data("MitoGenes")
 "MitoGenes"
diff --git a/R/dropletUtils_barcodeRank.R b/R/dropletUtils_barcodeRank.R
@@ -69,7 +69,8 @@ runBarcodeRankDrops <- function(inSCE,
                                 df = 20
 ) {
 
-  message(paste0(date(), " ... Running 'barcodeRanks'"))
+  p <- paste0(date(), " ... Running 'barcodeRanks'")
+  message(p)
 
   ##  Getting current arguments values
   argsList <- mget(names(formals()),sys.frame(sys.nframe()))

diff --git a/R/exportSCEtoAnndata.R b/R/exportSCEtoAnndata.R
@@ -54,7 +54,8 @@ exportSCEtoAnnData <- function(sce,
   fileName <- paste0(prefix,".h5ad")
   filePath <- file.path(outputDir,fileName)
   if (file.exists(filePath) && !isTRUE(overwrite)) {
-    stop(paste0(path, " already exists. Change 'outputDir' or set 'overwrite' to TRUE."))
+    p <- paste0(path, " already exists. Change 'outputDir' or set 'overwrite' to TRUE.")
+    stop(p)
   }
   if (isFALSE(forceDense)) {
     forceDense <- NULL

diff --git a/R/exportSCEtoTXT.R b/R/exportSCEtoTXT.R
@@ -40,7 +40,8 @@ exportSCEtoFlatFile <- function(sce,
 
 .checkOverwrite <- function(path, overwrite) {
   if (file.exists(path) && !isTRUE(overwrite)) {
-    stop(paste0(path, " already exists. Change 'outputDir' or set 'overwrite' to TRUE."))
+    p <- paste0(path, " already exists. Change 'outputDir' or set 'overwrite' to TRUE.")
+    stop(p)
   }
 }
 
@@ -86,7 +87,8 @@ exportSCEtoFlatFile <- function(sce,
 
       if(isTRUE(gzipped)) {
         .checkOverwrite(paste0(assaypath, ".gz"), overwrite)
-        message(date(), " .. Compressing into ", paste0(assaypath, ".gz"))
+        p <- paste0(assaypath, ".gz")
+        message(date(), " .. Compressing into ", p)
         R.utils::gzip(filename = assaypath, overwrite = overwrite)
       }
     }

diff --git a/R/getTopHVG.R b/R/getTopHVG.R
@@ -126,8 +126,9 @@ setTopHVG <- function(inSCE,
         }
     }
     rowSubset(inSCE, featureSubsetName) <- features
-    message(paste0(date(), " ... Feature subset variable '", featureSubsetName,
-                   "' created."))
+    p <- paste0(date(), " ... Feature subset variable '", featureSubsetName,
+                "' created.")
+    message(p)
     metadata(inSCE)$sctk$featureSubsets[[featureSubsetName]] <-
         list(method = method,
              number = nFeature,

diff --git a/R/ggPlotting.R b/R/ggPlotting.R
@@ -1089,7 +1089,8 @@ plotSCEViolinColData <- function(inSCE,
 
   if (!is.null(coldata)) {
     if (!coldata %in% names(SummarizedExperiment::colData(inSCE))) {
-      stop("'", paste(coldata), "' is not found in ColData.")
+      p <- paste(coldata)
+      stop("'", p, "' is not found in ColData.")
     }
     coldata <- SummarizedExperiment::colData(inSCE)[, coldata]
   } else {
@@ -1105,7 +1106,8 @@ plotSCEViolinColData <- function(inSCE,
       }
     } else {
       if (!groupBy %in% names(SummarizedExperiment::colData(inSCE))) {
-        stop("'", paste(groupBy), "' is not found in ColData.")
+        p <- paste(groupBy)
+        stop("'", p, "' is not found in ColData.")
       }
       groupBy <- as.character(SummarizedExperiment::colData(inSCE)[, groupBy])
     }
@@ -1314,7 +1316,8 @@ plotSCEViolinAssayData <- function(inSCE,
       }
     } else {
       if (!groupBy %in% names(SummarizedExperiment::colData(inSCE))) {
-        stop("'", paste(groupBy), "' is not found in ColData.")
+        p <- paste(groupBy)
+        stop("'", p , "' is not found in ColData.")
       }
       groupBy <- as.character(SummarizedExperiment::colData(inSCE)[, groupBy])
     }
@@ -1547,7 +1550,8 @@ plotSCEViolin <- function(inSCE,
       }
     } else {
       if (!groupBy %in% names(SummarizedExperiment::colData(inSCE))) {
-        stop("'", paste(groupBy), "' is not found in ColData.")
+        p <- paste(groupBy)
+        stop("'", p , "' is not found in ColData.")
       }
       groupBy <- SummarizedExperiment::colData(inSCE)[, groupBy]
     }
@@ -1768,7 +1772,8 @@ plotSCEDensityColData <- function(inSCE,
 
   if (!is.null(coldata)) {
     if (!coldata %in% names(SummarizedExperiment::colData(inSCE))) {
-      stop("'", paste(coldata), "' is not found in ColData.")
+      p <- paste(coldata)
+      stop("'", p , "' is not found in ColData.")
     }
     coldata <- SummarizedExperiment::colData(inSCE)[, coldata]
   } else {
@@ -1784,7 +1789,8 @@ plotSCEDensityColData <- function(inSCE,
       }
     } else {
       if (!groupBy %in% names(SummarizedExperiment::colData(inSCE))) {
-        stop("'", paste(groupBy), "' is not found in ColData.")
+        p <- paste(groupBy)
+        stop("'", p , "' is not found in ColData.")
       }
       groupBy <- as.character(SummarizedExperiment::colData(inSCE)[, groupBy])
     }
@@ -1939,7 +1945,8 @@ plotSCEDensityAssayData <- function(inSCE,
       }
     } else {
       if (!groupBy %in% names(SummarizedExperiment::colData(inSCE))) {
-        stop("'", paste(groupBy), "' is not found in ColData.")
+        p <- paste(groupBy)
+        stop("'", p , "' is not found in ColData.")
       }
       groupBy <- as.character(SummarizedExperiment::colData(inSCE)[, groupBy])
     }
@@ -2103,7 +2110,8 @@ plotSCEDensity <- function(inSCE,
       }
     } else {
       if (!groupBy %in% names(SummarizedExperiment::colData(inSCE))) {
-        stop("'", paste(groupBy), "' is not found in ColData.")
+        p <- paste(groupBy)
+        stop("'", p , "' is not found in ColData.")
       }
       groupBy <- as.character(SummarizedExperiment::colData(inSCE)[, groupBy])
     }
@@ -2640,7 +2648,8 @@ plotSCEBarColData <- function(inSCE,
                               combinePlot = TRUE) {
   if (!is.null(coldata)) {
     if (!coldata %in% names(SummarizedExperiment::colData(inSCE))) {
-      stop("'", paste(coldata), "' is not found in ColData.")
+      p <- paste(coldata)
+      stop("'", p , "' is not found in ColData.")
     }
     coldata <- SummarizedExperiment::colData(inSCE)[, coldata]
   } else {
@@ -2656,7 +2665,8 @@ plotSCEBarColData <- function(inSCE,
       }
     } else {
       if (!groupBy %in% names(SummarizedExperiment::colData(inSCE))) {
-        stop("'", paste(groupBy), "' is not found in ColData.")
+        p <- paste(groupBy)
+        stop("'", p , "' is not found in ColData.")
       }
       groupBy <- as.character(SummarizedExperiment::colData(inSCE)[, groupBy])
     }
@@ -2775,7 +2785,8 @@ plotSCEBarAssayData <- function(inSCE,
       }
     } else {
       if (!groupBy %in% names(SummarizedExperiment::colData(inSCE))) {
-        stop("'", paste(groupBy), "' is not found in ColData.")
+        p <- paste(groupBy)
+        stop("'", p , "' is not found in ColData.")
       }
       groupBy <- as.character(SummarizedExperiment::colData(inSCE)[, groupBy])
     }

diff --git a/R/htmlReports.R b/R/htmlReports.R
@@ -374,7 +374,8 @@ reportSeuratRun <- function(inSCE,
 
   path <- paste0(outputPath, "SCE_SeuratRun", "-", gsub(" ", "_", Sys.Date()), ".rds")
   saveRDS(data, path)
-  message("Output SCE object stored as ", paste0("SCE_SeuratRun", "-", gsub(" ", "_", Sys.Date()), ".rds"), " in ", outputPath, ".")
+  p <- paste0("SCE_SeuratRun", "-", gsub(" ", "_", Sys.Date()), ".rds")
+  message("Output SCE object stored as ", p , " in ", outputPath, ".")
   message("Output HTML file stored as ", outputFile, " in ", outputPath, ".")
 
   return(data)
@@ -506,7 +507,8 @@ reportSeuratResults <- function(inSCE,
 
   path <- paste0(outputPath, "SCE_SeuratResults", "-", gsub(" ", "_", Sys.Date()), ".rds")
   saveRDS(data, path)
-  message("Output SCE object stored as ", paste0("SCE_SeuratResults", "-", gsub(" ", "_", Sys.Date()), ".rds"), " in ", outputPath, ".")
+  p <- paste0("SCE_SeuratResults", "-", gsub(" ", "_", Sys.Date()), ".rds")
+  message("Output SCE object stored as ", p , " in ", outputPath, ".")
   message("Output HTML file stored as ", outputFile, " in ", outputPath, ".")
 
   return(data)
@@ -593,7 +595,8 @@ reportSeuratDimRed <- function(inSCE,
 
   path <- paste0(outputPath, "SCE_SeuratDimRed", "-", gsub(" ", "_", Sys.Date()), ".rds")
   saveRDS(data, path)
-  message("Output SCE object stored as ", paste0("SCE_SeuratDimRed", "-", gsub(" ", "_", Sys.Date()), ".rds"), " in ", outputPath, ".")
+  p <- paste0("SCE_SeuratDimRed", "-", gsub(" ", "_", Sys.Date()), ".rds")
+  message("Output SCE object stored as ", p , " in ", outputPath, ".")
   message("Output HTML file stored as ", outputFile, " in ", outputPath, ".")
 
   return(data)
@@ -660,7 +663,8 @@ reportSeuratNormalization <- function(inSCE,
 
   path <- paste0(outputPath, "SCE_SeuratNormalization", "-", gsub(" ", "_", Sys.Date()), ".rds")
   saveRDS(data, path)
-  message("Output SCE object stored as ", paste0("SCE_SeuratNormalization", "-", gsub(" ", "_", Sys.Date()), ".rds"), " in ", outputPath, ".")
+  p <- paste0("SCE_SeuratNormalization", "-", gsub(" ", "_", Sys.Date()), ".rds")
+  message("Output SCE object stored as ", p , " in ", outputPath, ".")
   message("Output HTML file stored as ", outputFile, " in ", outputPath, ".")
 
   return(data)
@@ -735,7 +739,8 @@ reportSeuratFeatureSelection <- function(inSCE,
 
   path <- paste0(outputPath, "SCE_SeuratFeatureSelection", "-", gsub(" ", "_", Sys.Date()), ".rds")
   saveRDS(data, path)
-  message("Output SCE object stored as ", paste0("SCE_SeuratFeatureSelection", "-", gsub(" ", "_", Sys.Date()), ".rds"), " in ", outputPath, ".")
+  p <- paste0("SCE_SeuratFeatureSelection", "-", gsub(" ", "_", Sys.Date()), ".rds")
+  message("Output SCE object stored as ", p , " in ", outputPath, ".")
   message("Output HTML file stored as ", outputFile, " in ", outputPath, ".")
 
   return(data)
@@ -802,7 +807,8 @@ reportSeuratScaling <- function(inSCE,
 
   path <- paste0(outputPath, "SCE_SeuratScaleData", "-", gsub(" ", "_", Sys.Date()), ".rds")
   saveRDS(data, path)
-  message("Output SCE object stored as ", paste0("SCE_SeuratScaleData", "-", gsub(" ", "_", Sys.Date()), ".rds"), " in ", outputPath, ".")
+  p <- paste0("SCE_SeuratScaleData", "-", gsub(" ", "_", Sys.Date()), ".rds")
+  message("Output SCE object stored as ", p , " in ", outputPath, ".")
   message("Output HTML file stored as ", outputFile, " in ", outputPath, ".")
 
   return(data)
@@ -914,7 +920,8 @@ reportSeuratClustering <- function(inSCE,
 
   path <- paste0(outputPath, "SCE_SeuratClustering", "-", gsub(" ", "_", Sys.Date()), ".rds")
   saveRDS(data, path)
-  message("Output SCE object stored as ", paste0("SCE_SeuratClustering", "-", gsub(" ", "_", Sys.Date()), ".rds"), " in ", outputPath, ".")
+  p <- paste0("SCE_SeuratClustering", "-", gsub(" ", "_", Sys.Date()), ".rds")
+  message("Output SCE object stored as ", p , " in ", outputPath, ".")
   message("Output HTML file stored as ", outputFile, " in ", outputPath, ".")
 
   return(data)
@@ -1018,7 +1025,8 @@ reportSeuratMarkerSelection <- function(inSCE,
 
   path <- paste0(outputPath, "SCE_SeuratResults", "-", gsub(" ", "_", Sys.Date()), ".rds")
   saveRDS(data, path)
-  message("Output SCE object stored as ", paste0("SCE_SeuratResults", "-", gsub(" ", "_", Sys.Date()), ".rds"), " in ", outputPath, ".")
+  p <- paste0("SCE_SeuratResults", "-", gsub(" ", "_", Sys.Date()), ".rds")
+  message("Output SCE object stored as ", p , " in ", outputPath, ".")
   message("Output HTML file stored as ", outputFile, " in ", outputPath, ".")
 
   return(data)
@@ -1184,7 +1192,8 @@ reportSeurat <- function(
 
   path <- paste0(outputPath, "SCE_SeuratReport", "-", gsub(" ", "_", Sys.Date()), ".rds")
   saveRDS(data, path)
-  message("Output SCE object stored as ", paste0("SCE_SeuratReport", "-", gsub(" ", "_", Sys.Date()), ".rds"), " in ", outputPath, ".")
+  p <- paste0("SCE_SeuratReport", "-", gsub(" ", "_", Sys.Date()), ".rds")
+  message("Output SCE object stored as ", p , " in ", outputPath, ".")
   message("Output HTML file stored as ", outputFile, " in ", outputPath, ".")
 
   return(data)

diff --git a/R/importExampleData.R b/R/importExampleData.R
@@ -58,7 +58,8 @@ importExampleData <- function(dataset, class = c("Matrix", "matrix"),
 
   if(dataset %in% scRNAseqDatasets) {
     if(!("scRNAseq" %in% rownames(utils::installed.packages()))) {
-      stop(paste0("Package 'scRNAseq' is not installed. Please install to load dataset '", dataset, "'."))
+      p <- paste0("Package 'scRNAseq' is not installed. Please install to load dataset '", dataset, "'.")
+      stop(p)
     }
     if (dataset == "fluidigm_pollen") {
       temp <- scRNAseq::ReprocessedFluidigmData()
@@ -84,7 +85,8 @@ importExampleData <- function(dataset, class = c("Matrix", "matrix"),
     }
   } else if (dataset %in% tenxPbmcDatasets) {
     if(!("TENxPBMCData" %in% rownames(utils::installed.packages()))) {
-      stop(paste0("Package 'TENxPBMCData' is not installed. Please install to load dataset '", dataset, "'."))
+      p <- paste0("Package 'TENxPBMCData' is not installed. Please install to load dataset '", dataset, "'.")
+      stop(p)
     }
     temp <- TENxPBMCData::TENxPBMCData(dataset = dataset)
     colnames(temp) <- paste(temp$Sample, temp$Barcode, sep="_")