Merge pull request #36 from michaelgruenstaeudl/testing

Improving output plot specs
michaelgruenstaeudl · Feb 28, 2024 · 633365e · 633365e
2 parents 3ccf9b0 + 06080ab
commit 633365e
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Showing 3 changed files with 41 additions and 37 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,7 +1,9 @@
 CHANGELOG
 ---------
-#### Version 1.0.9 (2024.02.28)
+
+#### Version 1.0.9 (2024.02.29)
 * Improving variable and file names
+* Correcting output plot specifications
 
 #### Version 1.0.8 (2024.02.28)
 * Handling of GenBank features with multiple qualifiers of the same name

diff --git a/R/helpers.R b/R/helpers.R
@@ -72,6 +72,37 @@ getPlotSpecs <- function(logScale,
   return(plotSpecs)
 }
 
+getOutputFields <- function(output) {
+  outputTypes <- paste(getOutputTypes(), collapse = "|")
+  outputPattern <- sprintf("^(?:.+\\.)(%s)$", outputTypes)
+  outputMatch <- regexec(outputPattern, output, ignore.case = TRUE)
+  outputVec <- regmatches(output, outputMatch)
+
+  # non-char `output` or non-match for char `output`
+  if ((length(outputVec) == 0) || (length(outputVec[[1]]) == 0)) {
+    output <- NULL
+    outputType <- NULL
+    isOutput <- FALSE
+  } else {
+    output <- outputVec[[1]][1]
+    outputType <- tolower(outputVec[[1]][2])
+    isOutput <- TRUE
+  }
+
+  outputFields <- list(
+    output = output,
+    outputType = outputType,
+    isOutput = isOutput
+  )
+  return(outputFields)
+}
+
+getOutputTypes <- function() {
+  outputTypes <- c("pdf",
+                   "png")
+  return(outputTypes)
+}
+
 filterByType <- function(x, typeFun) {
   if (typeFun(x)) {
     return(x)

diff --git a/R/visualisationOps.R b/R/visualisationOps.R
@@ -209,54 +209,25 @@ getLegendParams <- function(coverage,
   return(legendParams)
 }
 
-getOutputFields <- function(output) {
-  outputTypes <- paste(getOutputTypes(), collapse = "|")
-  outputPattern <- sprintf("^(?:.+\\.)(%s)$", outputTypes)
-  outputMatch <- regexec(outputPattern, output, ignore.case = TRUE)
-  outputVec <- regmatches(output, outputMatch)
-
-  # non-char `output` or non-match for char `output`
-  if ((length(outputVec) == 0) || (length(outputVec[[1]]) == 0)) {
-    output <- NULL
-    outputType <- NULL
-    isOutput <- FALSE
-  } else {
-    output <- outputVec[[1]][1]
-    outputType <- tolower(outputVec[[1]][2])
-    isOutput <- TRUE
-  }
-
-  outputFields <- list(
-    output = output,
-    outputType = outputType,
-    isOutput = isOutput
-  )
-  return(outputFields)
-}
-
 createVizFile <- function(plotSpecs) {
   output <- plotSpecs$output
   outputType <- plotSpecs$outputType
 
   if (outputType == "pdf") {
     pdf(output,
         width=10,
-        height=10)
+        height=10,
+        units="cm",
+        res=600)
   } else if (outputType == "png") {
     png(output,
-        width=480,
-        height=480)
+        width=10,
+        height=10,
+        units="cm",
+        res=600)
   }
 }
 
-getOutputTypes <- function() {
-  outputTypes <- c("pdf",
-                   "png")
-  return(outputTypes)
-}
-
-
-
 GenerateHistogramData <- function(region, coverage, windowSize, lastOne) {
     # Function to generate line data for RCircos.Line.Plot
     # ARGS: