Use palette functions from khroma

tesselle · Jul 26, 2024 · d86178d · d86178d
1 parent 69eecaf
commit d86178d
Show file tree

Hide file tree

Showing 30 changed files with 1,895 additions and 1,849 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -35,12 +35,12 @@ Imports:
     arkhe (>= 1.6.0),
     graphics,
     grDevices,
+    khroma (>= 1.13.0),
     methods,
     stats,
     utils
 Suggests: 
     folio (>= 1.4.0),
-    khroma (>= 1.12.0),
     knitr,
     markdown,
     rsvg,
@@ -52,7 +52,7 @@ VignetteBuilder:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Collate: 
     'AllClasses.R'
     'AllGenerics.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -5,6 +5,10 @@ S3method(labels,DiversityIndex)
 S3method(labels,RarefactionIndex)
 S3method(plot,DiversityIndex)
 S3method(plot,RarefactionIndex)
+export(color)
+export(palette_color_continuous)
+export(palette_color_discrete)
+export(palette_color_picker)
 export(remove_NA)
 export(remove_constant)
 export(remove_zero)
@@ -74,6 +78,10 @@ importFrom(arkhe,remove_zero)
 importFrom(arkhe,replace_NA)
 importFrom(arkhe,replace_zero)
 importFrom(arkhe,sparsity)
+importFrom(khroma,color)
+importFrom(khroma,palette_color_continuous)
+importFrom(khroma,palette_color_discrete)
+importFrom(khroma,palette_color_picker)
 importFrom(methods,.valueClassTest)
 importFrom(methods,as)
 importFrom(methods,callGeneric)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,6 @@
 # tabula 3.1.0.9000
+## Internals
+* Use palette functions from **khroma**.
 
 # tabula 3.1.0
 ## New classes and methods

diff --git a/R/plot_diversity.R b/R/plot_diversity.R
@@ -223,7 +223,7 @@ setMethod(
     ## Graphical parameters
     lwd <- list(...)$lwd %||% graphics::par("lwd")
     lty <- list(...)$lty %||% graphics::par("lty")
-    col <- list(...)$col %||% grDevices::hcl.colors(n, "viridis")
+    col <- list(...)$col %||% color("discreterainbow")(n)
     if (length(lwd) < n) lwd <- rep(lwd, length.out = n)
     if (length(lty) < n) lty <- rep(lty, length.out = n)
     if (length(col) < n) col <- rep(col, length.out = n)

diff --git a/R/plot_heatmap.R b/R/plot_heatmap.R
@@ -8,7 +8,8 @@ NULL
 setMethod(
   f = "plot_heatmap",
   signature = signature(object = "matrix"),
-  definition = function(object, col = grDevices::hcl.colors(12, "YlOrBr", rev = TRUE),
+  definition = function(object,
+                        col = color("YlOrBr")(12),
                         diag = TRUE, upper = TRUE, lower = TRUE,
                         freq = FALSE, margin = 1, fixed_ratio = TRUE,
                         axes = TRUE, legend = TRUE, ...) {
@@ -28,7 +29,8 @@ setMethod(
 setMethod(
   f = "plot_heatmap",
   signature = signature(object = "data.frame"),
-  definition = function(object, col = grDevices::hcl.colors(12, "YlOrBr", rev = TRUE),
+  definition = function(object,
+                        col = color("YlOrBr")(12),
                         diag = TRUE, upper = TRUE, lower = TRUE,
                         freq = FALSE, margin = 1, fixed_ratio = TRUE,
                         axes = TRUE, legend = TRUE, ...) {
@@ -47,7 +49,8 @@ setMethod(
 setMethod(
   f = "plot_heatmap",
   signature = signature(object = "dist"),
-  definition = function(object, col = grDevices::hcl.colors(12, "YlOrBr", rev = TRUE),
+  definition = function(object,
+                        col = color("YlOrBr")(12),
                         diag = FALSE, upper = FALSE, lower = !upper,
                         axes = TRUE, legend = TRUE, ...) {
     object <- as.matrix(object)

diff --git a/R/plot_matrix.R b/R/plot_matrix.R
@@ -287,8 +287,7 @@ prepare <- function(object, diag = TRUE, upper = TRUE, lower = TRUE,
   breaks <- pretty(val, n = 5)
   domain <- range(c(breaks, min_val, max_val))
   midpoint <- if (is.null(midpoint) & min_val < 0 & max_val > 0) 0 else midpoint
-  pal <- palette_color_continuous(colors = palette, domain = domain,
-                                            midpoint = midpoint)
+  pal <- palette_color_continuous(colors = palette, domain = domain, midpoint = midpoint)
   data$color <- if (length(palette) != length(val)) pal(val) else palette
 
   ## Clean data

diff --git a/R/plot_rank.R b/R/plot_rank.R
@@ -24,7 +24,7 @@ setMethod(
     lwd <- list(...)$lwd %||% graphics::par("lwd")
     lty <- list(...)$lty %||% graphics::par("lty")
     cex <- list(...)$cex %||% graphics::par("cex")
-    col <- list(...)$col %||% grDevices::hcl.colors(n, "viridis")
+    col <- list(...)$col %||% color("discreterainbow")(n)
     if (length(pch) < n) pch <- rep(pch, length.out = n)
     if (length(lwd) < n) lwd <- rep(lwd, length.out = n)
     if (length(lty) < n) lty <- rep(lty, length.out = n)

diff --git a/R/plot_spot.R b/R/plot_spot.R
@@ -9,7 +9,7 @@ setMethod(
   f = "plot_spot",
   signature = signature(object = "matrix"),
   definition = function(object, type = c("ring", "plain"),
-                        col = grDevices::hcl.colors(12, "YlOrBr", rev = TRUE),
+                        col = color("YlOrBr")(12),
                         diag = TRUE, upper = TRUE, lower = TRUE,
                         freq = FALSE, margin = 1,
                         axes = TRUE, legend = TRUE, ...) {
@@ -32,7 +32,7 @@ setMethod(
   f = "plot_spot",
   signature = signature(object = "data.frame"),
   definition = function(object, type = c("ring", "plain"),
-                        col = grDevices::hcl.colors(12, "YlOrBr", rev = TRUE),
+                        col = color("YlOrBr")(12),
                         diag = TRUE, upper = TRUE, lower = TRUE,
                         freq = FALSE, margin = 1,
                         axes = TRUE, legend = TRUE, ...) {
@@ -51,7 +51,7 @@ setMethod(
   f = "plot_spot",
   signature = signature(object = "dist"),
   definition = function(object, type = c("ring", "plain"),
-                        col = grDevices::hcl.colors(12, "YlOrBr", rev = TRUE),
+                        col = color("YlOrBr")(12),
                         diag = FALSE, upper = FALSE, lower = !upper,
                         axes = TRUE, legend = TRUE, ...) {
     # index_name <- attr(object, "method")

diff --git a/R/reexport.R b/R/reexport.R
@@ -23,3 +23,21 @@ arkhe::remove_constant
 #' @importFrom arkhe sparsity
 #' @export
 arkhe::sparsity
+
+# REEXPORT FROM KHROMA
+
+#' @importFrom khroma color
+#' @export
+khroma::color
+
+#' @importFrom khroma palette_color_continuous
+#' @export
+khroma::palette_color_continuous
+
+#' @importFrom khroma palette_color_discrete
+#' @export
+khroma::palette_color_discrete
+
+#' @importFrom khroma palette_color_picker
+#' @export
+khroma::palette_color_picker
diff --git a/codemeta.json b/codemeta.json
@@ -14,7 +14,7 @@
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.4.0 (2024-04-24)",
+  "runtimePlatform": "R version 4.4.1 (2024-06-14)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -100,19 +100,6 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=folio"
     },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "khroma",
-      "name": "khroma",
-      "version": ">= 1.12.0",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=khroma"
-    },
     {
       "@type": "SoftwareApplication",
       "identifier": "knitr",
@@ -217,23 +204,36 @@
       "name": "grDevices"
     },
     "5": {
+      "@type": "SoftwareApplication",
+      "identifier": "khroma",
+      "name": "khroma",
+      "version": ">= 1.13.0",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=khroma"
+    },
+    "6": {
       "@type": "SoftwareApplication",
       "identifier": "methods",
       "name": "methods"
     },
-    "6": {
+    "7": {
       "@type": "SoftwareApplication",
       "identifier": "stats",
       "name": "stats"
     },
-    "7": {
+    "8": {
       "@type": "SoftwareApplication",
       "identifier": "utils",
       "name": "utils"
     },
     "SystemRequirements": null
   },
-  "fileSize": "1567.133KB",
+  "fileSize": "1569.019KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",