Merge pull request #37 from HendrikSchultheis/download

Download

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: wilson
 Type: Package
 Title: Web-Based Interactive Omics Visualization
-Version: 2.3.0
+Version: 2.3.1
 Authors@R: c(
     person("Hendrik", "Schultheis", email = "hendrik.schultheis@mpi-bn.mpg.de", role = c("aut", "cre")),
     person("Jens", "Preussner", email = "jens.preussner@mpi-bn.mpg.de", role = "aut"),
@@ -16,7 +16,7 @@ LazyData: true
 Imports: shiny,
     data.table,
     ggplot2,
-    plotly,
+    plotly (> 4.8.0),
     scales,
     shinydashboard,
     DT (>= 0.3),
@@ -46,7 +46,8 @@ Imports: shiny,
     openssl,
     methods,
     R6,
-    magrittr
+    magrittr,
+    zip
 RoxygenNote: 6.1.1
 biocViews: 
 Suggests: knitr,

R/function.R

@@ -1207,7 +1207,7 @@ searchData <- function(input, choices, options = c("=", "<", ">"), min. = min(ch
 #' @param save_plot Logical if plot object should be saved as .RData.
 #' @param ui List of user inputs. Will be converted to JavaScript Object Notation. See \code{\link[RJSONIO]{toJSON}}
 #'
-#' @return See \code{\link[utils]{zip}}.
+#' @return Path to zip archive invisibly. See \code{\link[zip]{zipr}}.
 download <- function(file, filename, plot, width, height, ppi = 72, save_plot = TRUE, ui = NULL) {
   session <- shiny::getDefaultReactiveDomain()
 
@@ -1246,8 +1246,9 @@ download <- function(file, filename, plot, width, height, ppi = 72, save_plot =
     wd <- getwd()
     on.exit(setwd(wd)) # make sure working directory will be restored
     setwd(tempdir())
-    plotly::export(p = plot, file = plot_file_pdf)
-    plotly::export(p = plot, file = plot_file_png)
+    # Omit file path because orca adds it regardles of it already being there.
+    plotly::orca(p = plot, file = basename(plot_file_pdf))
+    plotly::orca(p = plot, file = basename(plot_file_png))
     setwd(wd)
   } else if (class(plot) == "Heatmap") { # TODO: find better way to check for complexHeatmap object
     # complexHeatmap
@@ -1288,7 +1289,7 @@ download <- function(file, filename, plot, width, height, ppi = 72, save_plot =
   }
 
   # create zip file
-  out <- utils::zip(zipfile = file, files = files, flags = "-j") # discard file path
+  out <- zip::zipr(zipfile = file, files = files, include_directories = FALSE)
 
   # remove tmp files
   file.remove(files)

R/parser.R

@@ -365,7 +365,13 @@ parser <- function(file, dec = ".") {
   names(metadata) <- as.character(metadata[1])
 
   # remove empty columns
-  metadata <- metadata[, which(unlist(lapply(metadata, function(x) !all(is.na(x) || x == "")))), with = FALSE]
+  empty_cols <- union(
+    which(colSums(is.na(metadata)) == nrow(metadata)), # indices of full na columns
+    which(colSums(metadata == "") == nrow(metadata)) # indices of full "" columns
+  )
+  if (length(empty_cols) > 0) {
+    metadata[, (empty_cols) := NULL]
+  }
 
   # delete first line
   metadata <- metadata[-1]