Support for PNG output

michaelgruenstaeudl · Feb 21, 2024 · 7c948d1 · 7c948d1
1 parent 0863972
commit 7c948d1
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Showing 3 changed files with 57 additions and 16 deletions.
diff --git a/R/PACVr.R b/R/PACVr.R
@@ -38,22 +38,24 @@ PACVr.visualizeWithRCircos <- function(gbkData,
                                        coverage,
                                        analysisSpecs,
                                        plotSpecs) {
-  if (plotSpecs$isOutput) {
-    logger::log_info('Generating a visualization of the sequencing coverage')
-    vizDoneSub <- "(including coverage)"
-    pdf(plotSpecs$output, width=10, height=10)
-  } else {
-    logger::log_info('No coverage data inferred; generating empty visualization')
-    vizDoneSub <- "(excluding coverage)"
+  logger::log_info('Generating a visualization of the sequencing coverage')
+  isOutput <- plotSpecs$isOutput
+
+  if (isOutput) {
+    createVizFile(plotSpecs)
   }
+
   visualizeWithRCircos(
     gbkData,
     coverage,
     analysisSpecs,
     plotSpecs
   )
-  dev.off()
-  logger::log_info('Visualization {vizDoneSub} saved as `{plotSpecs$output}`')
+
+  if (isOutput) {
+    dev.off()
+    logger::log_info('Visualization saved as `{plotSpecs$output}`')
+  }
 }
 
 #' @title Execute the complete pipeline of \pkg{PACVr}

diff --git a/R/helpers.R b/R/helpers.R
@@ -59,14 +59,16 @@ getPlotSpecs <- function(logScale,
                          relative,
                          textSize,
                          output) {
+  outputFields <- getOutputFields(output)
   plotSpecs <- list(
     logScale = filterLogical(logScale),
     threshold = filterPosNumeric(threshold),
     relative = filterLogical(relative),
     textSize = filterPosNumeric(textSize),
-    output = getOutput(output)
+    output = outputFields$output,
+    outputType = outputFields$outputType,
+    isOutput = outputFields$isOutput
   )
-  plotSpecs$isOutput <- !is.null(plotSpecs$output)
   return(plotSpecs)
 }
 

diff --git a/R/visualizeWithRCircos.R b/R/visualizeWithRCircos.R
@@ -42,7 +42,7 @@ visualizeWithRCircos <- function(gbkData,
     plotIRLinks(gbkData$linkData,
                 analysisSpecs$syntenyLineType)
   }
-  
+
   # STEP 6. GENERATE TITLE AND LEGEND
   logger::log_info('  Generating title and legend for visualization')
   graphics::title(paste(gbkData$plotTitle), line = -4.5, cex.main = 0.8)
@@ -209,10 +209,47 @@ getLegendParams <- function(coverage,
   return(legendParams)
 }
 
-getOutput <- function(output) {
-  if (is.character(output) && grepl("\\.pdf$", output, ignore.case = TRUE)) {
-    return(output)
+getOutputFields <- function(output) {
+  outputTypes <- paste(getOutputTypes(), collapse = "|")
+  outputPattern <- sprintf("^(?:.+\\.)(%s)$", outputTypes)
+  outputMatch <- regexec(outputPattern, output, ignore.case = TRUE)
+  outputVec <- regmatches(output, outputMatch)[[1]]
+
+  if (length(outputVec) == 0) {
+    output <- NULL
+    outputType <- NULL
+    isOutput <- FALSE
   } else {
-    return(NULL)
+    output <- outputVec[1]
+    outputType <- tolower(outputVec[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)
+  } else if (outputType == "png") {
+    png(output,
+        width=480,
+        height=480)
+  }
+}
+
+getOutputTypes <- function() {
+  outputTypes <- c("pdf",
+                   "png")
+  return(outputTypes)
 }