update and bugfix

SGDDNB · Oct 24, 2020 · 2b36efd · 2b36efd
1 parent 2425f22
commit 2b36efd
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Showing 27 changed files with 662 additions and 258 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -13,6 +13,7 @@ Depends:
     data.table   (>= 1.12.2),
     Matrix       (>= 1.2-17),
     hdf5r        (>= 1.2.0),
+    R.utils      (>= 2.8.0),
     ggplot2      (>= 3.3.0),
     grid                   ,
     gridExtra    (>= 2.3.0),

diff --git a/NAMESPACE b/NAMESPACE
@@ -4,6 +4,7 @@ export(addMeta)
 export(checkConfig)
 export(createConfig)
 export(delMeta)
+export(getExampleData)
 export(makeShinyApp)
 export(makeShinyCodes)
 export(makeShinyCodesMulti)

diff --git a/R/createConfig.R b/R/createConfig.R
@@ -27,7 +27,7 @@
 #' scConf = createConfig(obj)
 #'
 #' @export
-createConfig <- function(obj, meta.to.include = NA, legendCols = 3){
+createConfig <- function(obj, meta.to.include = NA, legendCols = 4){
   # Extract corresponding metadata
   if(class(obj)[1] == "Seurat"){
     objMeta = obj@meta.data

diff --git a/R/getExampleData.R b/R/getExampleData.R
@@ -0,0 +1,45 @@
+#' Download example Seurat objects
+#'
+#' Download example Seurat objects required for ShinyCell tutorial.
+#'
+#' @param type can be either "single" or "multi" which downloads one or two 
+#'   Seurat objects respectively for the Quick Start/Detailed Tutorial or 
+#'   Multi-dataset Tutorial respectively
+#' 
+#' @return downloaded Seurat object
+#'
+#' @author John F. Ouyang
+#'
+#' @import data.table
+#'
+#' @examples
+#' getExampleData()
+#'
+#' @export
+getExampleData <- function(type = c("single", "multi")){
+  # Setup and checks
+  files = c("http://files.ddnetbio.com/hrpiFiles/readySeu_rset.rds",
+            "http://files.ddnetbio.com/hrpiFiles/readySeu_d21i.rds")
+  names(files) = c("./readySeu_rset.rds", "./readySeu_d21i.rds")
+  if(type[1] == "single"){
+    files = files[1]
+  } else if(type[1] != "multi"){
+    stop("argument has to be either 'single' or 'multi'!")
+  }
+
+  # Download files
+  for(i in seq_along(files)){
+    if(!file.exists(names(files)[i])) {
+      res <- tryCatch(download.file(files[i],
+                                    destfile = names(files)[i],
+                                    method = "auto"),
+                      error = function(e) 1)
+      if(res == 1){ 
+        stop(paste0("Following file cannot be downloaded: ", names(files)[i]))
+      }
+    }
+  }
+  # return(scConf)
+}
+
+
diff --git a/R/makeShinyApp.R b/R/makeShinyApp.R
@@ -11,14 +11,13 @@
 #'   objects (v3+) or the "logcounts" assay for SingleCellExperiment objects
 #' @param gex.slot slot in single-cell assay to plot. This is only used 
 #'   for Seurat objects (v3+). Default is to use the "data" slot
-#' @param gene.mapping specify a mapping to convert gene identifiers. A 
-#'   named vector must be supplied where \code{names(gene.mapping)} correspond 
+#' @param gene.mapping specifies whether to convert Ensembl gene IDs (e.g. 
+#'   ENSG000xxx / ENSMUSG000xxx) into more "user-friendly" gene symbols. Set 
+#'   this to \code{TRUE} if you are using Ensembl gene IDs. Default is 
+#'   \code{FALSE} which is not to perform any conversion. Alternatively, users 
+#'   can supply a named vector where \code{names(gene.mapping)} correspond 
 #'   to the actual gene identifiers in the gene expression matrix whereas 
-#'   \code{gene.mapping} correspond to new identifiers to map to. Partial 
-#'   mapping is allowed where the mapping is only provided for some gene 
-#'   identifiers, the remaining gene identifiers will remain unchanged and a 
-#'   warning message will be presented. Default is \code{NA} which is not to 
-#'   perform any mapping
+#'   \code{gene.mapping} correspond to new identifiers to map to
 #' @param shiny.title title for shiny app
 #' @param shiny.footnotes text for shiny app footnote. Can be used to insert 
 #'   citations for the single-cell data
@@ -55,7 +54,7 @@
 #' @export
 makeShinyApp <- function(
   obj, scConf, gex.assay = NA, gex.slot = c("data", "scale.data", "counts"), 
-  gene.mapping = NA, 
+  gene.mapping = FALSE, 
   shiny.title = "scRNA-seq shiny app", shiny.footnotes = '""',
   shiny.dir = "shinyApp/", 
   default.gene1 = NA, default.gene2 = NA, default.multigene = NA, 

diff --git a/R/makeShinyCodes.R b/R/makeShinyCodes.R
@@ -25,26 +25,51 @@
 #' @export
 makeShinyCodes <- function(shiny.title, shiny.footnotes,
                            shiny.prefix, shiny.dir){
-  ### Write code for server.R
-  fname = paste0(shiny.dir, "/server.R")
-  readr::write_file(wrLib(
-    c("shiny","shinyhelper","data.table","Matrix","magrittr","ggplot2",
-      "hdf5r","ggdendro","gridExtra")), path = fname)
-  readr::write_file(wrSVload(shiny.prefix), append = TRUE, path = fname)
-  readr::write_file(wrSVfix(), append = TRUE, path = fname)
-  readr::write_file(wrSVmain(shiny.prefix), append = TRUE, path = fname)
-  readr::write_file(wrSVend(), append = TRUE, path = fname)
-
+  if(packageVersion("readr") >= "1.4.0"){
+    ### Write code for server.R
+    fname = paste0(shiny.dir, "/server.R")
+    readr::write_file(wrLib(
+      c("shiny","shinyhelper","data.table","Matrix","magrittr","ggplot2",
+        "hdf5r","ggdendro","gridExtra")), file = fname)
+    readr::write_file(wrSVload(shiny.prefix), append = TRUE, file = fname)
+    readr::write_file(wrSVfix(), append = TRUE, file = fname)
+    readr::write_file(wrSVmain(shiny.prefix), append = TRUE, file = fname)
+    readr::write_file(wrSVend(), append = TRUE, file = fname)
+
+
+    ### Write code for ui.R
+    fname = paste0(shiny.dir, "/ui.R")
+    readr::write_file(wrLib(
+      c("shiny","shinyhelper","data.table","Matrix","magrittr")), file = fname)
+    readr::write_file(wrUIload(shiny.prefix), append = TRUE, file = fname)
+    readr::write_file(wrUIsingle(shiny.title), append = TRUE, file = fname)
+    readr::write_file(wrUImain(shiny.prefix), append = TRUE, file = fname)
+    readr::write_file(glue::glue(', \n'), append = TRUE, file = fname)
+    readr::write_file(wrUIend(shiny.footnotes), append = TRUE, file = fname)
+
+  } else {
+    ### Write code for server.R
+    fname = paste0(shiny.dir, "/server.R")
+    readr::write_file(wrLib(
+      c("shiny","shinyhelper","data.table","Matrix","magrittr","ggplot2",
+        "hdf5r","ggdendro","gridExtra")), path = fname)
+    readr::write_file(wrSVload(shiny.prefix), append = TRUE, path = fname)
+    readr::write_file(wrSVfix(), append = TRUE, path = fname)
+    readr::write_file(wrSVmain(shiny.prefix), append = TRUE, path = fname)
+    readr::write_file(wrSVend(), append = TRUE, path = fname)
+
+
+    ### Write code for ui.R
+    fname = paste0(shiny.dir, "/ui.R")
+    readr::write_file(wrLib(
+      c("shiny","shinyhelper","data.table","Matrix","magrittr")), path = fname)
+    readr::write_file(wrUIload(shiny.prefix), append = TRUE, path = fname)
+    readr::write_file(wrUIsingle(shiny.title), append = TRUE, path = fname)
+    readr::write_file(wrUImain(shiny.prefix), append = TRUE, path = fname)
+    readr::write_file(glue::glue(', \n'), append = TRUE, path = fname)
+    readr::write_file(wrUIend(shiny.footnotes), append = TRUE, path = fname)
+  }
 
-  ### Write code for ui.R
-  fname = paste0(shiny.dir, "/ui.R")
-  readr::write_file(wrLib(
-    c("shiny","shinyhelper","data.table","Matrix","magrittr")), path = fname)
-  readr::write_file(wrUIload(shiny.prefix), append = TRUE, path = fname)
-  readr::write_file(wrUIsingle(shiny.title), append = TRUE, path = fname)
-  readr::write_file(wrUImain(shiny.prefix), append = TRUE, path = fname)
-  readr::write_file(glue::glue(', \n'), append = TRUE, path = fname)
-  readr::write_file(wrUIend(shiny.footnotes), append = TRUE, path = fname)
 }
 
 
diff --git a/R/makeShinyCodesMulti.R b/R/makeShinyCodesMulti.R
@@ -35,37 +35,73 @@ makeShinyCodesMulti <- function(shiny.title, shiny.footnotes,
     stop("length of shiny.prefix and shiny.headers does not match!")
   }
 
-  ### Write code for server.R
-  fname = paste0(shiny.dir, "/server.R")
-  readr::write_file(wrLib(
-    c("shiny","shinyhelper","data.table","Matrix","magrittr","ggplot2",
-      "hdf5r","ggdendro","gridExtra")), path = fname)
-  for(i in shiny.prefix){
-    readr::write_file(wrSVload(i), append = TRUE, path = fname)
+  if(packageVersion("readr") >= "1.4.0"){
+    ### Write code for server.R
+    fname = paste0(shiny.dir, "/server.R")
+    readr::write_file(wrLib(
+      c("shiny","shinyhelper","data.table","Matrix","magrittr","ggplot2",
+        "hdf5r","ggdendro","gridExtra")), file = fname)
+    for(i in shiny.prefix){
+      readr::write_file(wrSVload(i), append = TRUE, file = fname)
+    }
+    readr::write_file(wrSVfix(), append = TRUE, file = fname)
+    for(i in shiny.prefix){
+      readr::write_file(wrSVmain(i), append = TRUE, file = fname)
+    }
+    readr::write_file(wrSVend(), append = TRUE, file = fname)
+
+
+    ### Write code for ui.R
+    fname = paste0(shiny.dir, "/ui.R")
+    readr::write_file(wrLib(
+      c("shiny","shinyhelper","data.table","Matrix","magrittr")), file = fname)
+    for(i in shiny.prefix){
+      readr::write_file(wrUIload(i), append = TRUE, file = fname)
+    }
+    readr::write_file(wrUIsingle(shiny.title), append = TRUE, file = fname)
+    for(i in seq_along(shiny.prefix)){
+      hhh = shiny.headers[i]
+      readr::write_file(glue::glue('navbarMenu("{hhh}",'), 
+                        append = TRUE, file = fname)
+      readr::write_file(wrUImain(shiny.prefix[i]), append = TRUE, file = fname)
+      readr::write_file(glue::glue('), \n\n\n'), append = TRUE, file = fname)
+    }
+    readr::write_file(wrUIend(shiny.footnotes), append = TRUE, file = fname)
+
+  } else {
+    ### Write code for server.R
+    fname = paste0(shiny.dir, "/server.R")
+    readr::write_file(wrLib(
+      c("shiny","shinyhelper","data.table","Matrix","magrittr","ggplot2",
+        "hdf5r","ggdendro","gridExtra")), path = fname)
+    for(i in shiny.prefix){
+      readr::write_file(wrSVload(i), append = TRUE, path = fname)
+    }
+    readr::write_file(wrSVfix(), append = TRUE, path = fname)
+    for(i in shiny.prefix){
+      readr::write_file(wrSVmain(i), append = TRUE, path = fname)
+    }
+    readr::write_file(wrSVend(), append = TRUE, path = fname)
+
+
+    ### Write code for ui.R
+    fname = paste0(shiny.dir, "/ui.R")
+    readr::write_file(wrLib(
+      c("shiny","shinyhelper","data.table","Matrix","magrittr")), path = fname)
+    for(i in shiny.prefix){
+      readr::write_file(wrUIload(i), append = TRUE, path = fname)
+    }
+    readr::write_file(wrUIsingle(shiny.title), append = TRUE, path = fname)
+    for(i in seq_along(shiny.prefix)){
+      hhh = shiny.headers[i]
+      readr::write_file(glue::glue('navbarMenu("{hhh}",'), 
+                        append = TRUE, path = fname)
+      readr::write_file(wrUImain(shiny.prefix[i]), append = TRUE, path = fname)
+      readr::write_file(glue::glue('), \n\n\n'), append = TRUE, path = fname)
+    }
+    readr::write_file(wrUIend(shiny.footnotes), append = TRUE, path = fname)
   }
-  readr::write_file(wrSVfix(), append = TRUE, path = fname)
-  for(i in shiny.prefix){
-    readr::write_file(wrSVmain(i), append = TRUE, path = fname)
-  }
-  readr::write_file(wrSVend(), append = TRUE, path = fname)
-
 
-  ### Write code for ui.R
-  fname = paste0(shiny.dir, "/ui.R")
-  readr::write_file(wrLib(
-    c("shiny","shinyhelper","data.table","Matrix","magrittr")), path = fname)
-  for(i in shiny.prefix){
-    readr::write_file(wrUIload(i), append = TRUE, path = fname)
-  }
-  readr::write_file(wrUIsingle(shiny.title), append = TRUE, path = fname)
-  for(i in seq_along(shiny.prefix)){
-    hhh = shiny.headers[i]
-    readr::write_file(glue::glue('navbarMenu("{hhh}",'), 
-                      append = TRUE, path = fname)
-    readr::write_file(wrUImain(shiny.prefix[i]), append = TRUE, path = fname)
-    readr::write_file(glue::glue('), \n\n\n'), append = TRUE, path = fname)
-  }
-  readr::write_file(wrUIend(shiny.footnotes), append = TRUE, path = fname)
 }