Remove add.alpha()

git-svn-id: svn://scm.r-forge.r-project.org/svnroot/chnosz/pkg/CHNOSZ@830 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
jedick · Mar 2, 2024 · 9697071 · 9697071
1 parent 6702bef
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
-Date: 2024-02-28
+Date: 2024-03-02
 Package: CHNOSZ
-Version: 2.1.0-2
+Version: 2.1.0-3
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors@R: c(
     person("Jeffrey", "Dick", , "[email protected]", role = c("aut", "cre"),

diff --git a/NAMESPACE b/NAMESPACE
@@ -60,7 +60,7 @@ export(
 # added 20220416
   "rank.affinity",
 # added 20220620
-  "stack_mosaic", "add.alpha"
+  "stack_mosaic"
 )
 
 # Load shared objects
@@ -70,7 +70,7 @@ useDynLib(CHNOSZ, .registration = TRUE, .fixes = "C_")
 # Imports from default packages
 importFrom("grDevices", "dev.cur", "dev.off", "extendrange",
   "heat.colors", "png", "rainbow", "topo.colors", "dev.list",
-  "contourLines", "col2rgb", "rgb")
+  "contourLines", "col2rgb", "rgb", "adjustcolor")
 importFrom("graphics", "abline", "axTicks", "axis", "barplot", "box",
   "contour", "image", "legend", "lines", "mtext", "par", "plot",
   "plot.new", "plot.window", "points", "rect", "text", "title")

diff --git a/R/stack_mosaic.R b/R/stack_mosaic.R
@@ -10,7 +10,7 @@ stack_mosaic <- function(bases, species1, species2, species12, names = NULL, col
   loga_aq = NULL, plot.it = TRUE, ...) {
 
   # Default is to use semi-transparent fill for bimetallic species
-  if(is.null(fill)) fill <- list(NA, NA, add.alpha(col.names[3], "50"))
+  if(is.null(fill)) fill <- list(NA, NA, adjustcolor(col.names[3], alpha.f = 0.312))
 
   # Load species1 (first metal-bearing species)
   isp1 <- species(species1)

diff --git a/R/util.plot.R b/R/util.plot.R
@@ -296,11 +296,3 @@ thermo.axis <- function(lab = NULL, side = 1:4,line = 1.5, cex = par('cex'), lwd
     if(!is.null(lab)) mtext(lab, side = thisside, line = line, cex = cex, las = las)
   }
 }
-
-# Function to add transparency to given color 20220223
-add.alpha <- function(col, alpha) {
-  x <- col2rgb(col)
-  newcol <- rgb(x[1], x[2], x[3], maxColorValue = 255)
-  newcol <- paste0(newcol, alpha)
-  newcol
-}
diff --git a/README.md b/README.md
@@ -3,3 +3,7 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7765500.svg)](https://doi.org/10.5281/zenodo.7765500)
 [![R-CMD-check](https://github.com/jedick/CHNOSZ/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jedick/CHNOSZ/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
+
+This is a mirror of the [primary repository on R-Forge](https://r-forge.r-project.org/projects/chnosz/).
+
+Please see the [CHNOSZ website](https://chnosz.net) for more information.
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -15,11 +15,17 @@
 \newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{<I>C<sub>P</sub></I>}}{Cp}}}
 \newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{&Delta;<I>G</I>&deg;}}{ΔG°}}}
 
-\section{Changes in CHNOSZ version 2.1.0-2 (2024-02-28)}{
+\section{Changes in CHNOSZ version 2.1.0-3 (2024-03-02)}{
 
     \itemize{
+
       \item Move \code{read.fasta()}, \code{count.aa()}, and \code{aasum()} to canprot package.
+
       \item Remove \code{seq2aa()}.
+
+      \item Remove \code{add.alpha()}. Now \code{grDevices::adjustcolor()} is
+      used in \code{stack_mosaic()} to add transparency.
+
     }
 
 }

diff --git a/man/stack_mosaic.Rd b/man/stack_mosaic.Rd
@@ -47,8 +47,7 @@ Here, only a single value of \code{loga_aq} is needed, unlike in \code{\link{mos
 The plot parameters \code{col}, \code{col.names}, \code{fill}, \code{dx}, \code{dy}, \code{srt}, \code{lwd}, and \code{lty} should be length-3 lists (not vectors).
 The values of elements 1--3 of the list are recycled to the number of species in \code{species1}, \code{species2}, and \code{species12}, respectively.
 
-For \code{fill}, the default is to use no fill except for \code{species12}, where the fill color is taken from \code{col.names} with added transparency.
-The default definition of \code{fill} is \code{list(NA, NA, add.alpha(col.names[3], "50"))}.
+For \code{fill}, the default is to use no fill except for \code{species12}, where the fill color is taken from \code{col.names} with added transparency added using \code{\link{adjustcolor}}.
 }
 
 \section{Warning}{

diff --git a/man/util.plot.Rd b/man/util.plot.Rd
@@ -9,7 +9,6 @@
 \alias{water.lines}
 \alias{mtitle}
 \alias{ZC.col}
-\alias{add.alpha}
 \title{Functions to Create and Modify Plots}
 
 \description{
@@ -34,7 +33,6 @@
     lty = 2, lwd = 1, col = par("fg"), plot.it = TRUE)
   mtitle(main, line = 0, spacing = 1, ...)
   ZC.col(z)
-  add.alpha(col, alpha)
 }
 
 \arguments{
@@ -72,7 +70,6 @@
   \item{main}{character, text for plot title}
   \item{spacing}{numeric, spacing between multiple lines}
   \item{z}{numeric, set of values}
-  \item{alpha}{character, hexadecimal value of color transparency (alpha)}
 }
 
 \details{
@@ -107,8 +104,6 @@ This function exists to facilitate using \code{\link{expression}}s in multiline
 \code{ZC.col} uses \CRANpkg{colorspace}) to generate colors from a diverging palette (red - light grey - blue) corresponding to the values in \code{z}.
 Red is associated with lower values of \code{z}.
 This function is intended to generate colors for distinguishing average oxidation state of carbon \code{\link{ZC}}, but any numeric values can be supplied.
-
-\code{add.alpha} adds transparency to a color by appending the value of \code{alpha} to the hexadecimal representation of the color given in \code{col}.
 }
 
 \seealso{