From 6b4ea238555d09ae25d46d4199021f49781e280b Mon Sep 17 00:00:00 2001
From: Unknown <chelle.pierre@gmail.com>
Date: Thu, 19 May 2022 04:29:16 -0400
Subject: [PATCH 1/4] Fixes #273 NA are removed without producing warnings

---
 R/aaa-utilities.R                    |  2 ++
 R/plot-obs-vs-pred.R                 |  2 ++
 R/plot-res-vs-pred.R                 |  2 ++
 tests/testthat/test-no-na-warnings.R | 32 ++++++++++++++++++++++++++++
 4 files changed, 38 insertions(+)
 create mode 100644 tests/testthat/test-no-na-warnings.R

diff --git a/R/aaa-utilities.R b/R/aaa-utilities.R
index 6e15cdff..5991736b 100644
--- a/R/aaa-utilities.R
+++ b/R/aaa-utilities.R
@@ -113,6 +113,7 @@ parseAddScatterLayer <- function() {
           shape = mapLabels$shape
         ),
         size = getAestheticValues(n = 1, selectionKey = plotConfiguration$points$size, position = 0, aesthetic = "size"),
+        na.rm = TRUE,
         show.legend = TRUE
       )
   })
@@ -163,6 +164,7 @@ parseAddUncertaintyLayer <- function() {
           # Error bar size uses a ratio of 1/4 to match with point size
           size = getAestheticValues(n = 1, selectionKey = plotConfiguration$errorbars$size, position = 0, aesthetic = "size"),
           linetype = getAestheticValues(n = 1, selectionKey = plotConfiguration$errorbars$linetype, aesthetic = "linetype"),
+          na.rm = TRUE,
           show.legend = TRUE
         )
     }
diff --git a/R/plot-obs-vs-pred.R b/R/plot-obs-vs-pred.R
index a7a7c19e..7535895a 100644
--- a/R/plot-obs-vs-pred.R
+++ b/R/plot-obs-vs-pred.R
@@ -57,6 +57,7 @@ plotObsVsPred <- function(data,
         method = "loess",
         se = FALSE,
         formula = "y ~ x",
+        na.rm = TRUE,
         mapping = ggplot2::aes_string(x = mapLabels$x, y = mapLabels$y),
         color = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$color, position = lineIndex, aesthetic = "color"),
         linetype = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$linetype, position = lineIndex, aesthetic = "linetype"),
@@ -71,6 +72,7 @@ plotObsVsPred <- function(data,
         method = "lm",
         se = FALSE,
         formula = "y ~ x",
+        na.rm = TRUE,
         color = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$color, position = lineIndex, aesthetic = "color"),
         linetype = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$linetype, position = lineIndex, aesthetic = "linetype"),
         size = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$size, position = lineIndex, aesthetic = "size")
diff --git a/R/plot-res-vs-pred.R b/R/plot-res-vs-pred.R
index 0ef30e17..2ae20b10 100644
--- a/R/plot-res-vs-pred.R
+++ b/R/plot-res-vs-pred.R
@@ -47,6 +47,7 @@ plotResVsPred <- function(data,
         method = "loess",
         se = FALSE,
         formula = "y ~ x",
+        na.rm = TRUE,
         mapping = ggplot2::aes_string(x = mapLabels$x, y = mapLabels$y),
         color = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$color, position = lineIndex, aesthetic = "color"),
         linetype = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$linetype, position = lineIndex, aesthetic = "linetype"),
@@ -61,6 +62,7 @@ plotResVsPred <- function(data,
         method = "lm",
         se = FALSE,
         formula = "y ~ x",
+        na.rm = TRUE,
         color = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$color, position = lineIndex, aesthetic = "color"),
         linetype = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$linetype, position = lineIndex, aesthetic = "linetype"),
         size = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$size, position = lineIndex, aesthetic = "size")
diff --git a/tests/testthat/test-no-na-warnings.R b/tests/testthat/test-no-na-warnings.R
new file mode 100644
index 00000000..162ac464
--- /dev/null
+++ b/tests/testthat/test-no-na-warnings.R
@@ -0,0 +1,32 @@
+context("NA data are removed without warnings in scatter plots")
+
+# Test data that include a NA value
+testData <- data.frame(
+  x = c(1,2,3),
+  y = c(1,2,NA)
+)
+
+# To prevent copy/paste, expressions are used in the sequel
+plotNames <- c("TimeProfile", "ObsVsPred", "ResVsPred", "PKRatio", "DDIRatio")
+
+# Expression is "<plotname>DataMapping <- <PlotName>DataMapping$new()"
+createDataMapping <- parse(text = paste0(tolower(plotNames), "DataMapping <- ", plotNames, "DataMapping$new(x='x',y='y')"))
+eval(createDataMapping)
+
+# createPlot expression is "plot<PlotName>(data=testData, dataMapping=<plotname>DataMapping)"
+createPlot <- paste0("plot", plotNames, "(data=testData, dataMapping = ", tolower(plotNames), "DataMapping)")
+ggplotExpression <- parse(text = paste0('expect_is(', createPlot, ', "ggplot")'))
+warningExpression <- parse(text = paste0('expect_silent(', createPlot, ')'))
+
+
+test_that("Plot is produced as a ggplot object", {
+  expect_is(addScatter(data=testData), "ggplot")
+  expect_is(addLine(data=testData), "ggplot")
+  eval(ggplotExpression)
+})
+
+test_that("No warnings were produced when creating/printing the plot", {
+  expect_silent(addScatter(data=testData))
+  expect_silent(addLine(data=testData))
+  eval(warningExpression)
+})

From 921edff958bf1a463334a1ea81aa6161e5a16a58 Mon Sep 17 00:00:00 2001
From: Unknown <chelle.pierre@gmail.com>
Date: Thu, 19 May 2022 04:31:51 -0400
Subject: [PATCH 2/4] Fixes #272 set transparency for molecular plots

---
 R/aaa-utilities.R    | 3 +++
 R/plot-ddiratio.R    | 2 ++
 R/plot-obs-vs-pred.R | 2 ++
 R/plot-res-vs-pred.R | 2 ++
 4 files changed, 9 insertions(+)

diff --git a/R/aaa-utilities.R b/R/aaa-utilities.R
index 5991736b..23493f04 100644
--- a/R/aaa-utilities.R
+++ b/R/aaa-utilities.R
@@ -113,6 +113,7 @@ parseAddScatterLayer <- function() {
           shape = mapLabels$shape
         ),
         size = getAestheticValues(n = 1, selectionKey = plotConfiguration$points$size, position = 0, aesthetic = "size"),
+        alpha = getAestheticValues(n = 1, selectionKey = plotConfiguration$points$alpha, aesthetic = "alpha"),
         na.rm = TRUE,
         show.legend = TRUE
       )
@@ -141,6 +142,7 @@ parseAddLineLayer <- function(type, value, position) {
     ),
     "color=getAestheticValues(n=1,selectionKey=plotConfiguration$lines$color,position=", position, ',aesthetic="color"),',
     "linetype=getAestheticValues(n=1,selectionKey=plotConfiguration$lines$linetype,position=", position, ',aesthetic="linetype"),',
+    "alpha=getAestheticValues(n=1,selectionKey=plotConfiguration$lines$alpha,position=", position, ',aesthetic="alpha"),',
     "size=getAestheticValues(n=1,selectionKey=plotConfiguration$lines$size,position=", position, ', aesthetic="size"))'
   ))
 }
@@ -164,6 +166,7 @@ parseAddUncertaintyLayer <- function() {
           # Error bar size uses a ratio of 1/4 to match with point size
           size = getAestheticValues(n = 1, selectionKey = plotConfiguration$errorbars$size, position = 0, aesthetic = "size"),
           linetype = getAestheticValues(n = 1, selectionKey = plotConfiguration$errorbars$linetype, aesthetic = "linetype"),
+          alpha = getAestheticValues(n = 1, selectionKey = plotConfiguration$errorbars$alpha, aesthetic = "linetype"),
           na.rm = TRUE,
           show.legend = TRUE
         )
diff --git a/R/plot-ddiratio.R b/R/plot-ddiratio.R
index b00a9ca7..58f5beec 100644
--- a/R/plot-ddiratio.R
+++ b/R/plot-ddiratio.R
@@ -60,6 +60,7 @@ plotDDIRatio <- function(data,
       na.rm = TRUE,
       color = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$color, position = lineIndex, aesthetic = "color"),
       linetype = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$linetype, position = lineIndex, aesthetic = "linetype"),
+      alpha = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$alpha, position = lineIndex, aesthetic = "alpha"),
       size = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$size, position = lineIndex, aesthetic = "size")
     ) +
     ggplot2::geom_path(
@@ -68,6 +69,7 @@ plotDDIRatio <- function(data,
       na.rm = TRUE,
       color = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$color, position = lineIndex, aesthetic = "color"),
       linetype = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$linetype, position = lineIndex, aesthetic = "linetype"),
+      alpha = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$alpha, position = lineIndex, aesthetic = "alpha"),
       size = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$size, position = lineIndex, aesthetic = "size")
     )
 
diff --git a/R/plot-obs-vs-pred.R b/R/plot-obs-vs-pred.R
index 7535895a..18a040f1 100644
--- a/R/plot-obs-vs-pred.R
+++ b/R/plot-obs-vs-pred.R
@@ -61,6 +61,7 @@ plotObsVsPred <- function(data,
         mapping = ggplot2::aes_string(x = mapLabels$x, y = mapLabels$y),
         color = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$color, position = lineIndex, aesthetic = "color"),
         linetype = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$linetype, position = lineIndex, aesthetic = "linetype"),
+        alpha = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$alpha, position = lineIndex, aesthetic = "alpha"),
         size = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$size, position = lineIndex, aesthetic = "size")
       )
   }
@@ -75,6 +76,7 @@ plotObsVsPred <- function(data,
         na.rm = TRUE,
         color = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$color, position = lineIndex, aesthetic = "color"),
         linetype = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$linetype, position = lineIndex, aesthetic = "linetype"),
+        alpha = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$alpha, position = lineIndex, aesthetic = "alpha"),
         size = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$size, position = lineIndex, aesthetic = "size")
       )
   }
diff --git a/R/plot-res-vs-pred.R b/R/plot-res-vs-pred.R
index 2ae20b10..c061ebe9 100644
--- a/R/plot-res-vs-pred.R
+++ b/R/plot-res-vs-pred.R
@@ -51,6 +51,7 @@ plotResVsPred <- function(data,
         mapping = ggplot2::aes_string(x = mapLabels$x, y = mapLabels$y),
         color = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$color, position = lineIndex, aesthetic = "color"),
         linetype = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$linetype, position = lineIndex, aesthetic = "linetype"),
+        alpha = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$alpha, position = lineIndex, aesthetic = "alpha"),
         size = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$size, position = lineIndex, aesthetic = "size")
       )
   }
@@ -65,6 +66,7 @@ plotResVsPred <- function(data,
         na.rm = TRUE,
         color = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$color, position = lineIndex, aesthetic = "color"),
         linetype = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$linetype, position = lineIndex, aesthetic = "linetype"),
+        alpha = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$alpha, position = lineIndex, aesthetic = "alpha"),
         size = getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$size, position = lineIndex, aesthetic = "size")
       )
   }

From e5c5b560d242c596a84d423f3403059a09417c28 Mon Sep 17 00:00:00 2001
From: Unknown <chelle.pierre@gmail.com>
Date: Thu, 19 May 2022 04:40:13 -0400
Subject: [PATCH 3/4] Update line layer in scatter plots

---
 R/aaa-utilities.R        | 7 ++++---
 R/plot-ddiratio.R        | 4 ++--
 R/plot-obs-vs-pred.R     | 3 ++-
 R/plot-res-vs-pred.R     | 3 ++-
 man/parseAddLineLayer.Rd | 5 +++--
 5 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/R/aaa-utilities.R b/R/aaa-utilities.R
index 23493f04..156d851c 100644
--- a/R/aaa-utilities.R
+++ b/R/aaa-utilities.R
@@ -33,7 +33,7 @@ parseVariableFromObject <- function(objectName, variableName, keepIfNull = FALSE
 #' @return An expression to `eval()`
 #' @keywords internal
 parseValueToObject <- function(objectName, value) {
-  if (isOfLength(value, 0)) {
+  if (isEmpty(value)) {
     return(parse(text = paste0(objectName, " <- NULL")))
   }
   if (isOfType(value, "character")) {
@@ -122,11 +122,12 @@ parseAddScatterLayer <- function() {
 
 #' @title parseAddLineLayer
 #' @description Create an expression that adds scatter plot layer
+#' TODO: create a vignette explaining how argument `lines` in dataMapping is related to this
 #' @param type one of "horizontal", "vertical" or "diagonal"
 #' Note that for "diagonal", geom_abline is used.
 #' `value` of intercept is taken as is for linear scale but corresponds to the log of `value` for log scale.
-#'  For instance, intercept = c(-1, 0, 1) actually means that the line will go through c(0.1, 1, 10) for x=1
-#'  because log10(c(-1, 0, 1)) = c(0.1, 1, 10).
+#'  For instance, intercept = c(-1, 0, 1) with log scale actually means that the line will go through c(0.1, 1, 10)
+#'  because c(-1, 0, 1) = log10(c(0.1, 1, 10)).
 #' @param value value of xintercept or yintercept
 #' @param position line position for aesthetic properties
 #' @return An expression to `eval()`
diff --git a/R/plot-ddiratio.R b/R/plot-ddiratio.R
index 58f5beec..c4680944 100644
--- a/R/plot-ddiratio.R
+++ b/R/plot-ddiratio.R
@@ -42,12 +42,12 @@ plotDDIRatio <- function(data,
   if(residualsVsObserved){
     lineOrientation <- "ddiHorizontal"
   }
-  # Include horizontal lines
+  # Include diagonal or horizontal lines depending on the plot type
   for (lineIndex in seq_along(dataMapping$lines)) {
     # position correspond to the number of layer lines already added
     eval(parseAddLineLayer(lineOrientation, dataMapping$lines[[lineIndex]], lineIndex - 1))
   }
-  if (isOfLength(lineIndex, 0)) {
+  if (isEmpty(lineIndex)) {
     lineIndex <- 0
   }
   # Add Guest et al. lines to plot
diff --git a/R/plot-obs-vs-pred.R b/R/plot-obs-vs-pred.R
index 18a040f1..da5710aa 100644
--- a/R/plot-obs-vs-pred.R
+++ b/R/plot-obs-vs-pred.R
@@ -43,10 +43,11 @@ plotObsVsPred <- function(data,
 
   plotObject <- plotObject %||% initializePlot(plotConfiguration)
 
+  # Add diagonal lines with offset defined in lines of dataMapping
   for (lineIndex in seq_along(dataMapping$lines)) {
     eval(parseAddLineLayer("diagonal", dataMapping$lines[[lineIndex]], lineIndex - 1))
   }
-  if (isOfLength(lineIndex, 0)) {
+  if (isEmpty(lineIndex)) {
     lineIndex <- 0
   }
   # Add Smoother if defined
diff --git a/R/plot-res-vs-pred.R b/R/plot-res-vs-pred.R
index c061ebe9..1cbecc03 100644
--- a/R/plot-res-vs-pred.R
+++ b/R/plot-res-vs-pred.R
@@ -33,10 +33,11 @@ plotResVsPred <- function(data,
 
   plotObject <- plotObject %||% initializePlot(plotConfiguration)
 
+  # Add horizontal lines with offset defined in lines of dataMapping
   for (lineIndex in seq_along(dataMapping$lines)) {
     eval(parseAddLineLayer("horizontal", dataMapping$lines[[lineIndex]], lineIndex - 1))
   }
-  if (isOfLength(lineIndex, 0)) {
+  if (isEmpty(lineIndex)) {
     lineIndex <- 0
   }
   # Add Smoother if defined
diff --git a/man/parseAddLineLayer.Rd b/man/parseAddLineLayer.Rd
index 73cc2af9..dd9030d9 100644
--- a/man/parseAddLineLayer.Rd
+++ b/man/parseAddLineLayer.Rd
@@ -10,8 +10,8 @@ parseAddLineLayer(type, value, position)
 \item{type}{one of "horizontal", "vertical" or "diagonal"
 Note that for "diagonal", geom_abline is used.
 \code{value} of intercept is taken as is for linear scale but corresponds to the log of \code{value} for log scale.
-For instance, intercept = c(-1, 0, 1) actually means that the line will go through c(0.1, 1, 10) for x=1
-because log10(c(-1, 0, 1)) = c(0.1, 1, 10).}
+For instance, intercept = c(-1, 0, 1) with log scale actually means that the line will go through c(0.1, 1, 10)
+because c(-1, 0, 1) = log10(c(0.1, 1, 10)).}
 
 \item{value}{value of xintercept or yintercept}
 
@@ -22,5 +22,6 @@ An expression to \code{eval()}
 }
 \description{
 Create an expression that adds scatter plot layer
+TODO: create a vignette explaining how argument \code{lines} in dataMapping is related to this
 }
 \keyword{internal}

From 2944e702481568591d38ad8b494a91c50f72e4f9 Mon Sep 17 00:00:00 2001
From: Unknown <chelle.pierre@gmail.com>
Date: Thu, 19 May 2022 05:48:50 -0400
Subject: [PATCH 4/4] Fix typo

---
 R/aaa-utilities.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/aaa-utilities.R b/R/aaa-utilities.R
index 156d851c..749d9746 100644
--- a/R/aaa-utilities.R
+++ b/R/aaa-utilities.R
@@ -167,7 +167,7 @@ parseAddUncertaintyLayer <- function() {
           # Error bar size uses a ratio of 1/4 to match with point size
           size = getAestheticValues(n = 1, selectionKey = plotConfiguration$errorbars$size, position = 0, aesthetic = "size"),
           linetype = getAestheticValues(n = 1, selectionKey = plotConfiguration$errorbars$linetype, aesthetic = "linetype"),
-          alpha = getAestheticValues(n = 1, selectionKey = plotConfiguration$errorbars$alpha, aesthetic = "linetype"),
+          alpha = getAestheticValues(n = 1, selectionKey = plotConfiguration$errorbars$alpha, aesthetic = "alpha"),
           na.rm = TRUE,
           show.legend = TRUE
         )