Testing

CHANGELOG.md

@@ -4,6 +4,7 @@ CHANGELOG
 #### Version 1.0.9 (2024.02.29)
 * Improving variable and file names
 * Correcting output plot specifications
+* Increase logger use, improve logger format
 
 #### Version 1.0.8 (2024.02.28)
 * Handling of GenBank features with multiple qualifiers of the same name

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: PACVr
 Version: 1.0.9
-Date: 2024-02-28
+Date: 2024-02-29
 Title: Plastome Assembly Coverage Visualization
 Authors@R: c(person("Gregory", "Smith", role=c("ctb")),
              person("Nils", "Jenke", role=c("ctb")),

R/PACVr.R

@@ -83,7 +83,7 @@ PACVr.vizWithRCircos <- function(gbkData,
 #' value of the average coverage instead of an absolute value
 #' @param textSize a numeric value that specifies the relative font size of the 
 #' text element in the visualization
-#' @param verbose a boolean, that when TRUE, generates additional files with
+#' @param tabularCovStats a boolean, that when TRUE, generates additional files with
 #' detailed genomic region information
 #' @param output a character string that specifies the name of, and path to, 
 #' the output file
@@ -98,15 +98,15 @@ PACVr.vizWithRCircos <- function(gbkData,
 #' outFile <- paste(tempdir(), "/NC_045072__all_reads.pdf", sep="")
 #' PACVr.complete(gbkFile=gbkFile, bamFile=bamFile, windowSize=250, logScale=FALSE,
 #'                threshold=0.5, IRCheck=1, relative=TRUE, textSize=0.5,
-#'                verbose=FALSE, output=outFile)
+#'                tabularCovStats=FALSE, output=outFile)
 #' }
 #' \dontrun{
 #' gbkFile <- system.file("extdata", "MG936619/MG936619.gb", package="PACVr")
 #' bamFile <- system.file("extdata", "MG936619/MG936619_subsampled.bam", package="PACVr")
 #' outFile <- paste(tempdir(), "/MG936619_CoverageViz.pdf", sep="")
 #' PACVr.complete(gbkFile=gbkFile, bamFile=bamFile, windowSize=50, logScale=FALSE,
 #'                threshold=0.5, IRCheck=NA, relative=TRUE, textSize=0.5,
-#'                verbose=FALSE, output=outFile)
+#'                tabularCovStats=FALSE, output=outFile)
 #' }
 
 PACVr.complete <- function(gbkFile,
@@ -117,7 +117,7 @@ PACVr.complete <- function(gbkFile,
                            IRCheck=NA,
                            relative=TRUE,
                            textSize=0.5,
-                           verbose=FALSE,
+                           tabularCovStats=FALSE,
                            output=NA) {
   ######################################################################
   read.gbData <- PACVr.read.gb(gbkFile)
@@ -131,7 +131,6 @@ PACVr.complete <- function(gbkFile,
     logger::log_fatal('Parsing of any sequence features unsuccessful.')
     return(-1)
   }
-
   ###################################
   plotSpecs <- getPlotSpecs(logScale,
                             threshold,
@@ -145,7 +144,7 @@ PACVr.complete <- function(gbkFile,
                                  plotSpecs$logScale)
 
   ###################################
-  if (verbose) {
+  if (tabularCovStats) {
     PACVr.compileCovStats(gbkData,
                           coverage$raw,
                           analysisSpecs,

R/RCircosOps.R

@@ -42,19 +42,19 @@ PACVr.Histogram.Plot <- function(hist.data = NULL,
                                  genomic.columns = 3,
                                  is.sorted = TRUE) {
   if (is.null(hist.data)) {
-    warning("Genomic data missing in input.")
-    stop()
+    logger::log_error("Genomic data missing in input.")
+    stop() # Should 'stop()' be replaced with 'return(NULL)' ?
   }
   boundary <- RCircos::RCircos.Get.Plot.Boundary(track.num, side, inside.pos, outside.pos, FALSE)
   outerPos <- boundary[1]
   innerPos <- boundary[2]
   if (is.null(genomic.columns) || genomic.columns < 2 || genomic.columns > 3) {
-    warning("Number of columns for genomic position incorrect.")
-    stop()
+    logger::log_error("Number of columns for genomic position incorrect.")
+    stop() # Should 'stop()' be replaced with 'return(NULL)' ?
   }
   if (is.null(data.col) || data.col <= genomic.columns)  {
-    warning(paste("Number of input columns must be > ", genomic.columns, ".", sep=""))
-    stop()
+    logger::log_error(paste("Number of input columns must be > ", genomic.columns, ".", sep=""))
+    stop() # Should 'stop()' be replaced with 'return(NULL)' ?
   }
   RCircos.Pos <- RCircos::RCircos.Get.Plot.Positions()
   RCircos.Par <- RCircos::RCircos.Get.Plot.Parameters()
@@ -72,8 +72,8 @@ PACVr.Histogram.Plot <- function(hist.data = NULL,
     min.value <- min(histValues)
   } else {
     if (min.value > max.value) {
-      warning("min.value must be greater than max.value.")
-      stop()
+      logger::log_error("min.value must be greater than max.value.")
+	  stop() # Should 'stop()' be replaced with 'return(NULL)' ?
     }
   }
   histHeight <- RCircos::RCircos.Get.Data.Point.Height(histValues,

R/coverageCalcOps.R

@@ -13,8 +13,8 @@ CovCalc <- function(coverageRaw,
   # RETURNS:
   #     data.frame with region names, chromosome start, chromosome end and coverage calcucation
   if (!is.numeric(windowSize) | windowSize < 0) {
-    warning("User-selected window size must be >= 1.")
-    stop()
+    logger::log_error("User-selected window size must be >= 1.")
+    stop() # Should 'stop()' be replaced with 'return(NULL)' ?
   }
   bins <- GenomicRanges::tileGenome(
       sum(IRanges::runLength(coverageRaw)),

R/helpers.R

@@ -12,8 +12,8 @@ HistCol <- function(cov, threshold, relative, logScale) {
   #   color vector
   # Error handling
   if (!is.numeric(threshold) | threshold < 0) {
-    warning("User-defined coverage depth threshold must be >=1.")
-    stop()
+    logger::log_error("User-defined coverage depth threshold must be >=1.")
+    stop() # Should 'stop()' be replaced with 'return(NULL)' ?
   }
   if (relative == TRUE & logScale) {
     threshold <- mean(cov[, 4]) + log(threshold)

R/visualisationOps.R

@@ -216,15 +216,13 @@ createVizFile <- function(plotSpecs) {
   if (outputType == "pdf") {
     pdf(output,
         width=10,
-        height=10,
-        units="cm",
-        res=600)
+        height=10)
   } else if (outputType == "png") {
     png(output,
         width=10,
         height=10,
-        units="cm",
-        res=600)
+        units="in",
+        res=300)
   }
 }
 

inst/extdata/PACVr_Rscript.R

@@ -44,7 +44,7 @@ CmdLineArgs <- function() {
                               dest    = "threshold",
                               help    = "a numeric value that specifies the threshold for plotting coverage depth bars in red as opposed to the default black [default = %default]", 
                               metavar = "integer"),
-                  make_option(opt_str = c("-irc","--IRCheck"),
+                  make_option(opt_str = c("-i","--IRCheck"),
                               type    = "numeric", 
                               default = 1,
                               dest    = "IRCheck",
@@ -69,10 +69,10 @@ CmdLineArgs <- function() {
                               dest    = "textSize",
                               help    = "a numeric value that specifies the relative font size of the text element in the visualization [default = %default]", 
                               metavar = "integer"),
-                  make_option(opt_str = c("-v","--verbose"), 
+                  make_option(opt_str = c("-c","--tabularCovStats"), 
                               type    = "logical", 
                               default = FALSE, 
-                              dest    = "verbose",
+                              dest    = "tabularCovStats",
                               help    = paste("a boolean, that when TRUE, generates additional files with",
                                               "detailed genomic region information"),
                               metavar = "logical"),
@@ -111,7 +111,7 @@ PACVr.complete(gbkFile = opt$gbkFile,
                IRCheck = opt$IRCheck,
                relative = opt$relative,
                textSize = opt$textSize,
-               verbose = opt$verbose,
+               tabularCovStats = opt$tabularCovStats,
                output = opt$output)
 
 ########################################################################

inst/extdata/PACVr_run_parallel.R

@@ -25,29 +25,29 @@ run_PACVr <- function(f) {
   gbkFile <- paste0(inFileDir, basename(f))
   bamFile <- paste0(inFileDir, accNum, "_mapping_OneMoreLocations.sorted.bam")
 
-  tmpName <- paste0(inFileDir, accNum, "_CoverageViz_IRCheckFALSE")
-  #sink(paste0(tmpName, ".log"))
-  outFile <- paste0(tmpName, ".png")
-  PACVr.complete(gbkFile, bamFile, windowSize=250, logScale=FALSE, 
-                 threshold=0.5, relative=TRUE, textSize=0.5, 
-                 output=outFile)
-  #sink()
+#  tmpName <- paste0(inFileDir, accNum, "_CoverageViz_IRCheckFALSE")
+#  outFile <- paste0(tmpName, ".png")
+#  PACVr.complete(gbkFile, bamFile, windowSize=250, logScale=FALSE, 
+#                 threshold=0.5, relative=TRUE, textSize=0.5, 
+#                 output=outFile)
 
 #  tmpName <- paste0(inFileDir, accNum, "_CoverageViz_IRCheck0")
-#  sink(paste0(tmpName, ".log"))
 #  outFile <- paste0(tmpName, ".png")
 #  PACVr.complete(gbkFile, bamFile, windowSize=250, logScale=FALSE, 
 #                 threshold=0.5, relative=TRUE, textSize=0.5, 
 #                 IRCheck=0, output=outFile)
-#  sink()
 
-#  tmpName <- paste0(inFileDir, accNum, "_CoverageViz_IRCheck1")
-#  sink(paste0(tmpName, ".log"))
+  tmpName <- paste0(inFileDir, accNum, "_CoverageViz_IRCheck1")
+  outFile <- paste0(tmpName, ".png")
+  PACVr.complete(gbkFile, bamFile, windowSize=250, logScale=FALSE, 
+                 threshold=0.5, relative=TRUE, textSize=0.5, 
+                 IRCheck=1, output=outFile)
+
+#  tmpName <- paste0(inFileDir, accNum, "_CoverageViz_IRCheck1_withStats")
 #  outFile <- paste0(tmpName, ".png")
 #  PACVr.complete(gbkFile, bamFile, windowSize=250, logScale=FALSE, 
 #                 threshold=0.5, relative=TRUE, textSize=0.5, 
-#                 IRCheck=1, output=outFile)
-#  sink()
+#                 IRCheck=1, tabularCovStats=TRUE, output=outFile)
 }
 
 foreach(i=1:length(inFiles), .packages=c("PACVr")) %dopar% {

vignettes/PACVr_Vignette.Rnw

@@ -72,7 +72,7 @@ outFile <- paste(tempdir(), "/NC_045072_CoverageViz.pdf", sep="")
 PACVr.complete(gbkFile, bamFile, windowSize=250, 
            logScale=FALSE, threshold=0.5, syntenyLineType=1,
            relative=TRUE, textSize=0.5, regionsCheck=FALSE,
-           verbose=FALSE, output=outFile)
+           tabularCovStats=FALSE, output=outFile)
 \end{BGVerbatim}
 
 \subsection{Via Unix shell}