more pkgdown and palette updates

.Rbuildignore

@@ -4,3 +4,4 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^data-raw$

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: jakR
 Type: Package
 Title: jakR Miscellaneous Scripts
-Version: 0.11.11
+Version: 0.11.12
 Author: Jeff Kimbrel
 Date: 2018-06-12
 Maintainer: Jeff Kimbrel <jakpot@gmail.com>
@@ -15,3 +15,5 @@ Imports:
     ggplot2,
     tidyverse
 URL: https://jeffkimbrel.github.io/jakR/
+Depends: 
+    R (>= 2.10)

NAMESPACE

@@ -32,5 +32,4 @@ export(seqtab_stats)
 export(show_color_palette)
 export(sigCombine)
 export(summarySE)
-export(tol)
 export(zeroOTU)

R/palette_jak.R

@@ -0,0 +1,56 @@
+#' A full-service color palette creator
+#'
+#' These palettes can be used all over.
+#'
+#' @param n Number of colors to return
+#' @param colors An optional vector of rgb or colors to use. Overwrites `p`
+#' @param p A named color palette
+#' @param reverse A boolean for whether the palette should be reversed or not
+#'
+#' @export
+
+palette_jak = function(p = "bay",
+                       colors = NULL,
+                       n = 2,
+                       reverse = FALSE) {
+
+  if (is.null(colors)) {
+    cols = colorRampPalette(unname(unlist(jak_palettes[p])))(n)
+  } else {
+    if (all(all_are_valid_colors(colors))) {
+      cols = colorRampPalette(colors)(n)
+    } else {
+      stop("ERROR: one of the colors isn't valid")
+    }
+  }
+
+  if (isTRUE(reverse)) {
+    return(rev(cols))
+  } else {
+    return(cols)
+  }
+}
+
+
+#' Check if a string contains valid color strings
+#'
+#' @param x A vector of colors in rgb or text string
+#'
+#' @export
+
+all_are_valid_colors <- function(x) {
+  sapply(x, function(X) {
+    tryCatch(is.matrix(col2rgb(X)),
+             error = function(e) FALSE)
+  })
+}
+
+# palette_jak$jak = expand_named_palette(pal = c("blue" = "#037bcf",
+#                                                "red" = "#A81000",
+#                                                "yellow" = "#FFC00A",
+#                                                "green" = "#00A800",
+#                                                "darkblue" = "#002984",
+#                                                "purple" = "#4d0051",
+#                                                "black" = "#222222",
+#                                                "white" = "#EFEFEF")
+#                                        )

R/showColorPalette.R

@@ -35,3 +35,28 @@ show_color_palette = function(pal,
   p
 }
 
+#' Show all color palettes in the jak_palettes object
+#'
+#' @export
+
+show_all_color_palettes = function() {
+  input2 <- lapply(jak_palettes, as.data.frame, stringsAsFactors = FALSE)
+  df <- bind_rows(input2, .id = "Palette") |>
+    dplyr::select(Palette, RGB = `X[[i]]`)
+
+  df = df |>
+    group_by(Palette) |>
+    mutate(x = seq(n()))
+
+  df |>
+    ggplot(aes(x = x, y = Palette, fill = RGB)) +
+      theme_minimal() +
+      geom_tile() +
+      scale_fill_identity() +
+      scale_y_discrete(limits = rev)
+
+}
+
+
+
+

_pkgdown.yml

@@ -1,5 +1,58 @@
 url: https://jeffkimbrel.github.io/jakR/
 template:
   bootstrap: 5
-  bootswatch: sandstone
+  bslib:
+    bg: "#202123"
+    fg: "#B8BCC2"
+    primary: "#037bcf"
 
+reference:
+- title: Color Palettes
+  contents:
+  - palette_jak
+  - show_color_palette
+  - show_all_color_palettes
+  - expand_named_palette
+  - get_phylo_palette
+
+- title: Microbial Communities
+  contents:
+  - get_alpha_diversity
+  - get_phylo_diversity
+  - permanova
+  - pairwiseAdonis
+  - phylo_other
+  - plot_distances
+  - plotPD
+  - zeroOTU
+
+- title: Genomics
+  contents:
+  - fastq_filter_summary_amplicon
+  - fastq_info_summary
+  - run_fts
+  - get_fts_intervals
+  - plot_fts_intervals
+  - plot_fts_points
+  - getSig
+  - sigCombine
+  - orthofinder_complete_clusters
+  - orthofinder_summary
+  - drep_extract
+  - seqtab_stats
+
+- title: Misc
+  contents:
+  - jak_theme
+  - format_dt
+  - gt_theme
+
+- title: internal
+  contents:
+  - all_are_valid_colors
+  - getAlphaDiversity
+  - getPhyloDiversity
+  - jak_theme_black
+  - summarySE
+  - plotDistances
+  - jak_palettes

data-raw/jak_palettes.R

@@ -0,0 +1,40 @@
+## code to prepare `jak_palettes` dataset goes here
+
+jak_palettes = list(
+  "cb"            = c("#cc79a7","#0072b2","#56b4e9","#009e73","#f0e442","#e69f00","#d55e00"),
+
+  # from colorbook.io
+  "modernUI"      = c('#09D879','#0069FF','#D6D6D6','#FF4040','#FFDD00'),
+  "helpcenter"    = c('#E40035','#6900C5','#2F4AF9','#00BB6A','#8DC000','#FFC400','#FFAA3A','#FF662E','#FB4A4A'),
+  "bulma"         = c('#01D1B2','#5178FA','#3273DC','#23D160','#FFDD57','#FF3860'),
+  "blackdiamond"  = c('#6C7F50','#98C67C','#34557F','#FF635A','#D98626','#D3BF96','#685A5C','#786592','#78849C',
+                      '#DC443A','#ACDEE6','#EFBD47','#B0583A','#E2C2C7','#0088CE','#E9BF9B','#652D86','#512B1B',
+                      '#D1D4D3','#FE9666','#7BBBB2'),
+  "sachi"         = c('#005eac','#E7004C','#00C36B','#6D6462','#068CD6','#FE1E36','#F57C00','#0097A7','#A35FCA'),
+  "inslife"       = c('#80bec8','#6EB5C0','#e8e2e6','#FFCCBB','#83a0cd','#dee6f2','#DEAFB1','#AFDEDC','#DCC48E',
+                      '#CEB28D','#56CBF9','#E9D7C3'),
+  "pastelrainbow" = c('#E8CACA','#FFE5A8','#F8FF97','#BCFFA4','#A6FFD3','#B9E3FF','#C1CCFF','#E4CFFF','#F1CEF4'),
+
+  # from https://github.com/karthik/wesanderson
+  "zissou"        = c("#000000","#3B9AB2","#78B7C5","#EBCC2A","#E1AF00","#F21A00"),
+
+  # from PNW colors (https://github.com/jakelawlor/PNWColors)
+  "bay"           = c('#00496f','#0f85a0','#edd746','#ed8b00','#dd4124'),
+  "winter"        = c('#2d2926','#33454e','#537380','#81a9ad','#ececec'),
+  "lake"          = c('#362904','#54450f','#45681e','#4a9152','#64a8a8','#85b6ce','#cde5f9','#eef3ff'),
+  "sailboat"      = c('#6e7cb9','#7bbcd5','#d0e2af','#f5db99','#e89c81','#d2848d'),
+
+  # from Paul Tol (https://personal.sron.nl/~pault/data/colourschemes.pdf)
+  "bright"        = c("#4477AA","#66CCEE","#228833","#CCBB44","#EE6677","#AA3377","#BBBBBB"),
+  "highContrast"  = c("#FFFFFF","#DDAA33","#BB5566","#004488","#000000"),
+  "vibrant"       = c("#007788","#33BBEE","#009988","#EE7733","#CC3311","#EE3377","#BBBBBB"),
+  "muted"         = c("#332288","#88ccee","#44aa99","#117733","#999933","#ddcc77","#cc6677","#882255","#aa4499"),
+  "pale"          = c("#bbccee","#cceeff","#ccddaa","#eeeebb","#ffcccc","#dddddd"),
+  "dark"          = c("#222255","#225555","#225522","#666633","#663333","#555555"),
+  "light"         = c("#77aadd","#99ddff","#44bb99","#bbcc33","#aaaa00","#eedd88","#ee8866","#ffaabb","#dddddd"),
+  "sunset"        = c("#364b9a","#4a7bb7","#6ea6cd","#98cae1","#c2e4ef","#eaeccc","#feda8b","#fdb366","#f67e4b","#dd3d2d","#a50026"),
+  "rainbow"       = c("#d1bbd7","#ae76a3","#882e72","#1965b0","#5289c7","#7bafde","#4eb265","#90c987","#cae0ab","#f7f056","#f6c141","#f1932d","#e8601c","#dc050c"),
+  "earth"         = c("#5566aa","#117733","#44aa66","#55aa22","#668822","#99bb55","#558877","#88bbaa","#aaddcc","#44aa88","#ddcc66","#ffdd44","#ffee88","#bb0011")
+)
+
+usethis::use_data(jak_palettes, overwrite = TRUE)