v1.1.0

New features: DATASET_STYLE, DATASET_COLORSTRIP, TREE_COLORS range, DATASET_SYMBOL, DATASET_DOMAINS, DATASET_CONNECTION, DATASET_MULTIBAR, DATASET_BINARY, DATASET_TEXT, DATASET_EXTERNALSHAPE, DATASET_PIECHART support full color palette(table2itol wesanderson npg aaas nejm lancet jama jco ucscgb d3 igv locuszoom uchicago simpsons futurama rickandmorty startrek tron gsea material BrBG PiYG PRGn PuOr RdBu RdGy RdYlBu RdYlGn Spectral Accent Dark2 Paired Pastel1 Pastel2 Set1 Set2 Set3 Blues BuGn BuPu GnBu Greens Greys Oranges OrRd PuBu PuBuGn PuRd Purples RdPu Reds YlGn YlGnBu YlOrBr YlOrRd) user level add DATASET_MULTIBAR, DATASET_LINECHART, DATASET_PIECHART, DATASET_ALIGNMENT, DATASET_IMAGE, POPUP_INFO support create_hub supports direct input of phylo objects for the tree parameter, not just the tree file path Fixed: wesanderson color palette random picking function changed from `runif` to `sample`, fixed the problem of repeated color matching
TongZhou2017 · Feb 12, 2023 · b122be0 · b122be0
1 parent 8ee489e
commit b122be0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: itol.toolkit
 Title: Helper Functions for 'Interactive Tree Of Life'
-Version: 1.0.5
+Version: 1.1.0
 Authors@R: 
     person(
     given = "Tong",
@@ -32,7 +32,9 @@ Imports:
     miniUI,
     shiny,
     rstudioapi,
-    colourpicker
+    colourpicker,
+    ggsci,
+    RColorBrewer
 Suggests: 
     knitr,
     rmarkdown,

diff --git a/NAMESPACE b/NAMESPACE
@@ -62,7 +62,9 @@ exportClasses(itol.theme)
 exportClasses(itol.unit)
 exportMethods("+")
 exportMethods(show)
+import(RColorBrewer)
 import(dplyr)
+import(ggsci)
 import(miniUI)
 import(rstudioapi)
 import(shiny)

diff --git a/R/object.R b/R/object.R
@@ -50,7 +50,10 @@ itol.hub <- setClass(
 #' create_hub(tree = TREE)
 #'
 create_hub <- function(tree,field_tree=NULL,seq=NULL,abundance=NULL,taxonomy=NULL,node_data=NULL,tip_data=NULL) {
-  tree <- list(main = read.tree(tree), field = list())
+  if (is.character(tree)) {
+    tree <- read.tree(tree)
+  }
+  tree <- list(main = tree, field = list())
   if (any(duplicated(tree$main$node.label)) || is.null(tree$main$node.label)) {
     tree$main <- ape::makeNodeLabel(phy = tree$main, method = "number", prefix = "I")
   }

diff --git a/R/user.R b/R/user.R
diff --git a/R/utils.R b/R/utils.R
@@ -71,10 +71,13 @@ correct_get_color <- function(str) {
 #' @return a vector of colors
 #' @importFrom wesanderson wes_palettes
 #' @importFrom stats runif
+#' @import ggsci
+#' @import RColorBrewer
 #' @export
-get_color <- function(n,set="table2itol") {
+get_color <- function(n=0,set="table2itol") {
   # Colour vectors collected by Jan P. Meier-Kolthoff.
   #
+
   COLOURS <- list(
     # Dark2; colour-blind-safe
     JMK01 = "#1b9e77",
@@ -328,6 +331,10 @@ get_color <- function(n,set="table2itol") {
       "#ceb8d4", "#635b2d", "#c79783", "#733426", "#476682", "#98762e"
     )
   )
+  if(set == "table2itol"){
+    return(COLOURS[[n]])
+  }
+  set_names <- c("table2itol")
   if(set == "wesanderson"){
     COLOURS <- list()
     colors_vector <- unique(unlist(wesanderson::wes_palettes))
@@ -344,11 +351,56 @@ get_color <- function(n,set="table2itol") {
                                                              "#35274A",
                                                              "#550307"))]
     for (i in 1:length(colors_vector)) {
-      indexs <- round(runif(n,1,length(colors_vector)))
+      indexs <- sample(1:length(colors_vector),n,replace=F)
       COLOURS[[i]] <- colors_vector[indexs]
     }
+    return(COLOURS[[n]])
+  }
+  set_names <- c(set_names,"wesanderson")
+  set_main <- stringr::str_remove(set, "_.*$")
+  ggsci_db<-utils::getFromNamespace("ggsci_db", "ggsci")
+  if(set_main %in% names(ggsci_db)){
+    if(grepl("_",set)){
+      set_type <- unlist(strsplit(set,"_"))
+      colors <- ggsci_db[[set_type[1]]][[set_type[2]]]
+    }else{
+      colors <- ggsci_db[[set]][[1]]
+    }
+    if(n > length(colors)){
+      warning("The pattern length is shorter than n. Appending default colors to
+              make the pattern length same with n.")
+      colors <- c(colors,COLOURS[[n-length(colors)]])
+    }
+    if(n < length(colors)){
+      warning("The pattern length is longer than n. The length is cutting as
+              same as n.")
+      colors <- colors[1:n]
+    }
+    return(colors)
+  }
+  set_names <- c(set_names,names(ggsci_db))
+  if(set %in% rownames(RColorBrewer::brewer.pal.info)){
+    n_max <- RColorBrewer::brewer.pal.info[set,]$maxcolors
+    if(n > n_max){
+      warning("The pattern length is shorter than n. Appending default colors to
+              make the pattern length same with n.")
+      colors <- RColorBrewer::brewer.pal(n=n_max,name = set)
+      colors <- c(colors,COLOURS[[n-n_max]])
+    }
+    if(n < n_max){
+      warning("The pattern length is longer than n. The length is cutting as
+              same as n.")
+      colors <- RColorBrewer::brewer.pal(n=n,name = set)
+    }
+    if(n == n_max){
+      colors <- RColorBrewer::brewer.pal(n=n,name = set)
+    }
+    return(colors)
+  }
+  set_names <- c(set_names,rownames(RColorBrewer::brewer.pal.info))
+  if(set == "ls"){
+    return(set_names)
   }
-  return(COLOURS[[n]])
 }
 
 #' Paste rows

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/Get_Start.html b/docs/articles/Get_Start.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   Get_Start: Get_Start.html
-last_built: 2023-02-05T05:28Z
+last_built: 2023-02-12T12:15Z
 
diff --git a/docs/reference/complex_html_text.html b/docs/reference/complex_html_text.html
diff --git a/docs/reference/convert_01.html b/docs/reference/convert_01.html
diff --git a/docs/reference/convert_01_to_connect.html b/docs/reference/convert_01_to_connect.html
diff --git a/docs/reference/convert_range_to_node.html b/docs/reference/convert_range_to_node.html
diff --git a/docs/reference/correct_get_color.html b/docs/reference/correct_get_color.html
diff --git a/docs/reference/count_to_tree.html b/docs/reference/count_to_tree.html
diff --git a/docs/reference/create_hub.html b/docs/reference/create_hub.html
diff --git a/docs/reference/create_theme.html b/docs/reference/create_theme.html
diff --git a/docs/reference/create_unit.html b/docs/reference/create_unit.html
diff --git a/docs/reference/df_merge.html b/docs/reference/df_merge.html
diff --git a/docs/reference/fa_read.html b/docs/reference/fa_read.html
diff --git a/docs/reference/fa_write.html b/docs/reference/fa_write.html
diff --git a/docs/reference/file_get_dir.html b/docs/reference/file_get_dir.html
diff --git a/docs/reference/file_get_name.html b/docs/reference/file_get_name.html
diff --git a/docs/reference/file_to_unit.html b/docs/reference/file_to_unit.html
diff --git a/docs/reference/get_color.html b/docs/reference/get_color.html
diff --git a/docs/reference/head_line.html b/docs/reference/head_line.html
diff --git a/docs/reference/hub_to_unit.html b/docs/reference/hub_to_unit.html