diff w4mcorcov_util.R @ 0:23f9fad4edfc draft

planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/w4mcorcov_util.R	Mon Oct 16 14:56:52 2017 -0400
@@ -0,0 +1,88 @@
+# tryCatchFunc wraps an expression that produces a value if it does not stop:
+#   tryCatchFunc produces a list
+#   On success of expr(), tryCatchFunc produces
+#     list(success TRUE, value = expr(), msg = "")
+#   On failure of expr(), tryCatchFunc produces
+#     list(success = FALSE, value = NA, msg = "the error message")
+tryCatchFunc <- function(expr) {
+  # format error for logging
+  format_error <- function(e) {
+    paste(c("Error { message:", e$message, ", call:", e$call, "}"), collapse = " ")
+  }
+  retval <- NULL
+  tryCatch(
+    expr = {
+      retval <- ( list( success = TRUE, value = eval(expr = expr), msg = "" ) )
+    }
+    , error = function(e) {
+      retval <<- list( success = FALSE, value = NA, msg = format_error(e) )
+    }
+  )
+  return (retval)
+}
+
+# turn off all plotting devices
+dev.off.all <- function() {
+  while (!is.null(dev.list())) { dev.off() }
+}
+  
+# capture plot and write to PDF; then close any devices opened in the process
+plot2pdf <- function(
+  file.name
+, plot.function
+, width = 12
+, height = 12
+) {
+  # capture plot and write to PDF
+  cur.dev <- dev.list()
+  filename <- file.name
+  pdf(file = filename, width = width, height = height)
+  plot.function()
+  # close any devices opened in the process
+  dev.off()
+  if (is.null(cur.dev)) {
+      dev.off.all()
+  } else {
+      while ( length(dev.list()) > length(cur.dev) ) { dev.off() }
+  }
+}
+
+# print and capture plot and write to PDF; then close any devices opened in the process
+#   This is needed for ggplot which does not print the plot when invoked within a function.
+print2pdf <- function(
+  file.name
+, plot.function
+, width = 12
+, height = 12
+) {
+  plot2pdf(
+    file.name = file.name
+  , width = width
+  , height = height
+  , plot.function = function() {
+      print(plot.function())
+    }
+  )
+}
+
+iso8601.znow <- function()
+{
+  strftime(as.POSIXlt(Sys.time(), "UTC"), "%Y-%m-%dT%H:%M:%SZ")
+}
+
+# pdf.name <- function(name)
+# {
+#   paste0(name, "_", iso8601.filename.fragment(), ".pdf")
+# }
+#
+# tsv.name <- function(name)
+# {
+#   paste0(name, "_", iso8601.filename.fragment(), ".tsv")
+# }
+#
+# # pseudo-inverse - computational inverse non-square matrix a
+# p.i <- function(a) {
+#   solve(t(a) %*% a) %*% t(a)
+# } 
+
+