Add some more tests, ignore lines that are not recognized by covr

Author: csoneson

R/plotPairs.R

@@ -126,13 +126,15 @@ plotPairs <- function(se, selAssay = "counts", doLog = TRUE, pseudocount = 1,
                     cols)(transfCor),
                     maxColorValue = 255)
             } else {
+                # nocov start
                 cols <- hcl.colors(n = 11, palette = "RdBu")[6:10]
                 col <- rgb(colorRamp(
                     cols)(transfCor),
                     maxColorValue = 255)
+                # nocov end
             }
         } else {
-            col <- "white"
+            col <- "white" #nocov
         }
 
         ## Construct plot
@@ -150,6 +152,9 @@ plotPairs <- function(se, selAssay = "counts", doLog = TRUE, pseudocount = 1,
     ## --------------------------------------------------------------------- ##
     ## Scatter plots
     ## --------------------------------------------------------------------- ##
+    # All the point plotting functions are tested, but for some reason covr 
+    # doesn't pick it up - ignore these definitions in the coverage tests
+    # nocov start
     if (pointsType == "smoothscatter") {
         ## Define function to create smoothscatter-like plot 
         ## (for use with ggpairs)
@@ -229,6 +234,7 @@ plotPairs <- function(se, selAssay = "counts", doLog = TRUE, pseudocount = 1,
             }
         }
     }
+    # nocov end
 
     ## Define the function to use for the plots
     if (pointsType == "smoothscatter") {
@@ -244,6 +250,7 @@ plotPairs <- function(se, selAssay = "counts", doLog = TRUE, pseudocount = 1,
     ## --------------------------------------------------------------------- ##
     ## Histogram
     ## --------------------------------------------------------------------- ##
+    # nocov start
     diaghist <- function(data, mapping, ...) {
         gg <- ggplot(data = data, mapping = mapping) +
             geom_histogram(fill = "#F5C710", color = "grey50", 
@@ -254,6 +261,7 @@ plotPairs <- function(se, selAssay = "counts", doLog = TRUE, pseudocount = 1,
         }
         gg
     }
+    # nocov end
 
     ## --------------------------------------------------------------------- ##
     ## Combined plot

R/plotResults.R

@@ -62,7 +62,7 @@
     .assertScalar(x = interactivePlot, type = "logical")
 
     if (interactivePlot && !requireNamespace("plotly", quietly = TRUE)) {
-        stop("The 'plotly' package is required to make interactive plots.")
+        stop("The 'plotly' package is required to make interactive plots.") # nocov
     }
     xr <- range(res[[xCol]], na.rm = TRUE)
     yr <- range(res[[yCol]], na.rm = TRUE)
@@ -113,7 +113,7 @@
         }
     }
     if (interactivePlot) {
-        plotly::ggplotly(gg)
+        plotly::ggplotly(gg) # nocov
     } else {
         if (!is.null(labelCol) && length(labelValues) > 0) {
             .assertVector(x = labelValues, type = "character", 

tests/testthat/test_linkMultipleVariants.R

@@ -535,6 +535,60 @@ test_that("linkMultipleVariants works", {
     expect_equal(res$filtSeparate$V3[, "nbrRetained"], 
                  sum(!grepl("C.*mut|del|V3\\.", truth$truth$status)))
 
+    # --------------------------------------------------------------------------
+    # Get warning when summing UMIs
+    expect_warning({
+        res <- linkMultipleVariants(
+            combinedDigestParams = list(
+                fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
+                                           package = "mutscan"),
+                fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
+                                           package = "mutscan"),
+                elementsForward = "UVCVCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
+                elementsReverse = "CVCV", elementLengthsReverse = c(6, 40, 10, -1),
+                mergeForwardReverse = TRUE, minOverlap = 20, 
+                maxOverlap = 30, maxFracMismatchOverlap = 0,
+                revComplForward = FALSE, revComplReverse = TRUE,
+                avePhredMinForward = 20, avePhredMinReverse = 20,
+                verbose = verbose),
+            barcode = list(
+                fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
+                                           package = "mutscan"),
+                elementsForward = "CVCSCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
+                avePhredMinForward = 20, 
+                collapseMaxDist = 1, collapseMinScore = 1, collapseMinRatio = 1,
+                verbose = verbose),
+            V2 = list(
+                fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
+                                           package = "mutscan"),
+                fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
+                                           package = "mutscan"),
+                elementsForward = "CSCVCS", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
+                elementsReverse = "CSCV", elementLengthsReverse = c(6, 40, 10, -1),
+                mergeForwardReverse = TRUE, minOverlap = 10, 
+                maxOverlap = 20, maxFracMismatchOverlap = 0,
+                revComplForward = FALSE, revComplReverse = TRUE,
+                avePhredMinForward = 20, avePhredMinReverse = 20,
+                wildTypeForward = truth$WTV2,
+                nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1, 
+                forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
+                verbose = verbose, useTreeWTmatch = TRUE),
+            V3 = list(
+                fastqForward = system.file("extdata", "multipleVariableRegions_R1.fastq.gz",
+                                           package = "mutscan"),
+                fastqReverse = system.file("extdata", "multipleVariableRegions_R2.fastq.gz",
+                                           package = "mutscan"),
+                elementsForward = "CSCSCV", elementLengthsForward = c(6, 24, 10, 30, 10, -1),
+                elementsReverse = "CVCS", elementLengthsReverse = c(6, 40, 10, -1),
+                mergeForwardReverse = TRUE, minOverlap = 5, 
+                maxOverlap = 15, maxFracMismatchOverlap = 0,
+                revComplForward = FALSE, revComplReverse = TRUE,
+                avePhredMinForward = 20, avePhredMinReverse = 20,
+                wildTypeForward = truth$WTV3,
+                nbrMutatedCodonsMaxForward = -1, nbrMutatedBasesMaxForward = 1, 
+                forbiddenMutatedCodonsForward = "", collapseToWTForward = FALSE,
+                verbose = verbose, useTreeWTmatch = TRUE)
+        )}, "Aggregating UMI counts")
 })