Make it possible to disable plotting in test

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: QDNAseq
-Version: 1.41.2-9001
+Version: 1.41.2-9002
 Title: Quantitative DNA Sequencing for Chromosomal Aberrations
 Depends: R (>= 3.1.0)
 Imports:

tests/QDNAseq.R

@@ -2,50 +2,55 @@ library(QDNAseq)
 library(Biobase) ## combine(), sampleNames()
 library(utils)
 
+do_plot <- TRUE
+do_cleanup <- TRUE
+
 # Load data
 data(LGG150)
 data <- LGG150
 print(data)
 stopifnot(inherits(data, "QDNAseqReadCounts"))
 
 # Plot isobars of read counts
-isobarPlot(data)
+if (do_plot) isobarPlot(data)
 
 # Plot copy number profile
-plot(data, ylim=c(-100, 200))
-highlightFilters(data, residual=TRUE, blacklist=TRUE)
+if (do_plot) {
+  plot(data, ylim=c(-100, 200))
+  highlightFilters(data, residual=TRUE, blacklist=TRUE)
+}
 
 # Filter out "bad" bins
 dataF <- applyFilters(data, residual=TRUE, blacklist=TRUE)
 print(dataF)
-plot(dataF, ylim=c(-100, 200))
+if (do_plot) plot(dataF, ylim=c(-100, 200))
 stopifnot(inherits(dataF, "QDNAseqReadCounts"))
 
 # Correct read counts as a function of GC content and mappability
 dataC <- correctBins(dataF)
 print(dataC)
-plot(dataC, ylim=c(-100, 200))
+if (do_plot) plot(dataC, ylim=c(-100, 200))
 stopifnot(inherits(dataC, "QDNAseqCopyNumbers"))
 
 # Normalize binned read counts to have diploid normal copy number
 dataN <- normalizeBins(dataC)
 print(dataN)
-plot(dataN)
+if (do_plot) plot(dataN)
 stopifnot(inherits(dataN, "QDNAseqCopyNumbers"))
 
 # Plot noise
-noisePlot(dataF)
+if (do_plot) noisePlot(dataF)
 
 # Segment copy numbers
 fit <- segmentBins(dataN)
 print(fit)
-plot(fit)
+if (do_plot) plot(fit)
 stopifnot(inherits(fit, "QDNAseqCopyNumbers"))
 
 # Call copy-number segments
 fitC <- callBins(fit)
 print(fitC)
-plot(fitC)
+if (do_plot) plot(fitC)
 
 
 # ---------------------------------------------------------------
@@ -75,8 +80,10 @@ for (name in names(sets)) {
         message(sprintf("    File(s) written: [n=%d] %s",
                 length(file), paste(sQuote(file), collapse = ", ")))
         stopifnot(all(file_test("-f", file)))
-        file.remove(file)
-        stopifnot(!any(file_test("-f", file)))
+        if (do_cleanup) {f
+	  file.remove(file)
+          stopifnot(!any(file_test("-f", file)))
+	}
       }
     }
   }
@@ -115,8 +122,10 @@ for (name in names(sets)) {
         message(sprintf("    File(s) written: [n=%d] %s",
                 length(file), paste(sQuote(file), collapse = ", ")))
         stopifnot(all(file_test("-f", file)))
-        file.remove(file)
-        stopifnot(!any(file_test("-f", file)))
+        if (do_cleanup) {
+          file.remove(file)
+          stopifnot(!any(file_test("-f", file)))
+	}  
       }
     }
   }