Fixes Open-Systems-Pharmacology#272 set transparency for molecular plots

pchelle · May 19, 2022 · 921edff · 921edff
1 parent 6b4ea23
commit 921edff
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diff --git 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
@@ -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
@@ -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
@@ -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")
       )
   }