diff --git a/DESCRIPTION b/DESCRIPTION
index f3c117a..0df2504 100644
--- 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
index ff876f1..bdc7b65 100644
--- 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
index afc2081..38a6bad 100644
--- 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
index 95a2e12..0b8614c 100644
--- a/R/user.R
+++ b/R/user.R
@@ -344,7 +344,7 @@ create_unit <- function(data,key,type,style="default",subtype=NULL,color=NULL,li
color = "table2itol"
}
if(length(color) == 1){
- if(color %in% c("table2itol","RColorBrewer", "ggsci", "wesanderson")){
+ if(stringr::str_remove(color,"_.*$") %in% get_color(set="ls")){
color_levels = get_color(length(unique(data[[colname_data]])),set = color)
color = as.factor(data[[colname_data]])
levels(color) <- color_levels
@@ -627,8 +627,8 @@ create_unit <- function(data,key,type,style="default",subtype=NULL,color=NULL,li
color = "table2itol"
}
if(length(color) == 1){
- if(color %in% c("table2itol","RColorBrewer", "ggsci")){
- color_levels = get_color(length(unique(data[[colname_data]])))
+ if(stringr::str_remove(color,"_.*$") %in% get_color(set="ls")){
+ color_levels = get_color(length(unique(data[[colname_data]])),set = color)
color = as.factor(data[[colname_data]])
levels(color) <- color_levels
}else {
@@ -668,6 +668,9 @@ create_unit <- function(data,key,type,style="default",subtype=NULL,color=NULL,li
profile$name <- key
unit <- new("itol.unit", type = type, sep = sep, profile = profile, field = field, common_themes = common_themes, specific_themes = specific_themes, data = data_left)
}
+ }
+ if (type == "DATASET_RANGE"){
+
}
if(type == "LABELS"){
if(!is.data.frame(data)){
@@ -768,8 +771,8 @@ create_unit <- function(data,key,type,style="default",subtype=NULL,color=NULL,li
color = "table2itol"
}
if(length(color) == 1){
- if(color %in% c("table2itol","RColorBrewer", "ggsci")){
- color_levels = get_color(length(unique(data[[colname_data]])))
+ if(stringr::str_remove(color,"_.*$") %in% get_color(set="ls")){
+ color_levels = get_color(length(unique(data[[colname_data]])),set = color)
color = as.factor(data[[colname_data]])
levels(color) <- color_levels
}else {
@@ -842,7 +845,7 @@ create_unit <- function(data,key,type,style="default",subtype=NULL,color=NULL,li
color = "table2itol"
}
if(length(color) == 1){
- if(color %in% c("table2itol","RColorBrewer", "ggsci", "wesanderson")){
+ if(stringr::str_remove(color,"_.*$") %in% get_color(set="ls")){
color_levels = get_color(length(unique(data[[colname_data]])),set = color)
color = as.factor(data[[colname_data]])
levels(color) <- color_levels
@@ -883,7 +886,15 @@ create_unit <- function(data,key,type,style="default",subtype=NULL,color=NULL,li
data_left[["tip"]] <- df_merge(data_left[["tip"]], data)
field_length <- length(field_names)
field$labels <- field_names
- field$colors <- get_color(field_length)
+ if(is.null(color)){
+ message("Using default color pattern: table2itol")
+ color = "table2itol"
+ }
+ if(stringr::str_remove(color,"_.*$") %in% get_color(set="ls")){
+ field$colors <- get_color(field_length,set = color)
+ }else{
+ field$colors <- get_color(field_length)
+ }
field$shapes <- rep(2,field_length)
unit <- new("itol.unit", type = type, sep = sep, profile = profile, field = field, common_themes = common_themes, specific_themes = specific_themes, data = data_left)
}
@@ -1052,8 +1063,8 @@ create_unit <- function(data,key,type,style="default",subtype=NULL,color=NULL,li
color = "table2itol"
}
if(length(color) == 1){
- if(color %in% c("table2itol","RColorBrewer", "ggsci")){
- color_levels = get_color(length(unique(data[[colname_data]])))
+ if(stringr::str_remove(color,"_.*$") %in% get_color(set="ls")){
+ color_levels = get_color(length(unique(data[[colname_data]])),set = color)
color = as.factor(data[[colname_data]])
levels(color) <- color_levels
}else {
@@ -1111,7 +1122,15 @@ create_unit <- function(data,key,type,style="default",subtype=NULL,color=NULL,li
data_left[["node"]] <- df_merge(data_left[["node"]], data)
data_left[["tip"]] <- df_merge(data_left[["tip"]], data)
field$labels <- field_names
- field$colors <- get_color(length(field_names))
+ if(is.null(color)){
+ message("Using default color pattern: table2itol")
+ color = "table2itol"
+ }
+ if(stringr::str_remove(color,"_.*$") %in% get_color(set="ls")){
+ field$colors <- get_color(field_length,set = color)
+ }else{
+ field$colors <- get_color(field_length)
+ }
profile$name <- key
sep = "\t"
unit <- new("itol.unit", type = type, sep = sep, profile = profile, field = field, common_themes = common_themes, specific_themes = specific_themes, data = data_left)
@@ -1214,8 +1233,8 @@ create_unit <- function(data,key,type,style="default",subtype=NULL,color=NULL,li
color = "table2itol"
}
if(length(color) == 1){
- if(color %in% c("table2itol","RColorBrewer", "ggsci")){
- color_levels = get_color(length(unique(data[[colname_data]])))
+ if(stringr::str_remove(color,"_.*$") %in% get_color(set="ls")){
+ color_levels = get_color(length(unique(data[[colname_data]])),set = color)
color = as.factor(data[[colname_data]])
levels(color) <- color_levels
}else {
@@ -1291,6 +1310,36 @@ create_unit <- function(data,key,type,style="default",subtype=NULL,color=NULL,li
specific_themes$basic_plot$dataset_scale <- c(min,mean,max)
unit <- new("itol.unit", type = type, sep = sep, profile = profile, field = field, common_themes = common_themes, specific_themes = specific_themes, data = data_left)
}
+ if(type == "DATASET_MULTIBAR"){
+ if(!is.data.frame(data)){
+ stop("The input data class should be a data frame")
+ }
+ if(names(data)[1] != "id"){
+ message(paste0("Using the first column as id: ",names(data)[1]))
+ names(data)[1] <- "id"
+ }
+ if(length(names(data)) < 2){
+ stop("The input data should has at least 2 columns")
+ }
+ field_names <- names(data)[-1]
+ names(data) <- c("id",paste0(key,"$",field_names))
+ data <- convert_range_to_node(data, tree)
+ data_left[["node"]] <- df_merge(data_left[["node"]], data)
+ data_left[["tip"]] <- df_merge(data_left[["tip"]], data)
+ field_length <- length(field_names)
+ field$labels <- field_names
+ if(is.null(color)){
+ message("Using default color pattern: table2itol")
+ color = "table2itol"
+ }
+ if(stringr::str_remove(color,"_.*$") %in% get_color(set="ls")){
+ field$colors <- get_color(field_length,set = color)
+ }else{
+ field$colors <- get_color(field_length)
+ }
+ profile$name <- key
+ unit <- new("itol.unit", type = type, sep = sep, profile = profile, field = field, common_themes = common_themes, specific_themes = specific_themes, data = data_left)
+ }
if(type=="DATASET_BOXPLOT"){
if(!is.data.frame(data)){
stop("The input data class should be a data frame")
@@ -1327,6 +1376,104 @@ create_unit <- function(data,key,type,style="default",subtype=NULL,color=NULL,li
specific_themes$basic_plot$dataset_scale <- c(min,mean,max)
unit <- new("itol.unit", type = type, sep = sep, profile = profile, field = field, common_themes = common_themes, specific_themes = specific_themes, data = data_left)
}
+ if(type == "DATASET_LINECHART"){
+ if(!is.data.frame(data)){
+ stop("The input data class should be a data frame")
+ }
+ if(names(data)[1] != "id"){
+ message(paste0("Using the 1st column as id: ",names(data)[1]))
+ names(data)[1] <- "id"
+ }
+ if(names(data)[2] != "X"){
+ message(paste0("Using the 2nd column as X: ",names(data)[2]))
+ names(data)[2] <- "X"
+ }
+ if(names(data)[3] != "Y"){
+ message(paste0("Using the 3rd column as Y: ",names(data)[3]))
+ names(data)[3] <- "Y"
+ }
+ if(length(names(data)) != 3){
+ stop("The input data should has 3 columns: id, x, y")
+ }
+ names(data) <- c("id",paste0(key,c("$X", "$Y")))
+ data <- convert_range_to_node(data, tree)
+ data_left[["node"]] <- df_merge(data_left[["node"]], data)
+ data_left[["tip"]] <- df_merge(data_left[["tip"]], data)
+ profile$name <- key
+ specific_themes$linechart$basic$x <- ""
+ specific_themes$linechart$basic$y <- ""
+ unit <- new("itol.unit", type = type, sep = sep, profile = profile, field = field, common_themes = common_themes, specific_themes = specific_themes, data = data_left)
+ }
+ if(type == "DATASET_PIECHART"){
+ if(!is.data.frame(data)){
+ stop("The input data class should be a data frame")
+ }
+ if(names(data)[1] != "id"){
+ message(paste0("Using the 1st column as id: ",names(data)[1]))
+ names(data)[1] <- "id"
+ }
+ if(is.null(position)){
+ message(paste0("Using the 2nd column as position: ",names(data)[2]))
+ names(data)[2] <- "POSITION"
+ }else{
+ data <- data.frame(data[,1],POSITION=position,data[,2:ncol(data)])
+ }
+ if(is.null(size_factor)){
+ message(paste0("Using the 3rd column as radius: ",names(data)[3]))
+ names(data)[3] <- "RADIUS"
+ }else {
+ data <- data.frame(data[,1:2],RADIUS=size_factor,data[,3:ncol(data)])
+ }
+ field_names <- names(data)[-c(1:3)]
+ names(data) <- c("id",paste0(key,"$",c("POSITION", "RADIUS",field_names)))
+ data <- convert_range_to_node(data, tree)
+ data_left[["node"]] <- df_merge(data_left[["node"]], data)
+ data_left[["tip"]] <- df_merge(data_left[["tip"]], data)
+ field_length <- length(field_names)
+ field$labels <- field_names
+ if(is.null(color)){
+ message("Using default color pattern: table2itol")
+ color = "table2itol"
+ }
+ if(stringr::str_remove(color,"_.*$") %in% get_color(set="ls")){
+ field$colors <- get_color(field_length,set = color)
+ }else{
+ field$colors <- get_color(field_length)
+ }
+ profile$name <- key
+ unit <- new("itol.unit", type = type, sep = sep, profile = profile, field = field, common_themes = common_themes, specific_themes = specific_themes, data = data_left)
+ }
+ if(type == "DATASET_ALIGNMENT"){
+ if(!is.data.frame(data)){
+ if(file.exists(data)){
+ fasta_file <- Biostrings::readBStringSet(data)
+ NODE_ID <- names(fasta_file)
+ SEQUENCE <- paste(fasta_file)
+ df_data <- data.frame(NODE_ID, SEQUENCE)
+ df_data$NODE_ID <- as.character(df_data$NODE_ID)
+ names(df_data) <- c("id",paste0(key,c("$SEQUENCE")))
+ }
+ stop("The input data class should be a data frame or a alignment file")
+ }else {
+ if(length(names(data)) > 2){
+ message("The input data should be 2 column: id, seq")
+ }
+ df_data <- data[,1:2]
+ df_data[,1] <- as.character(df_data[,1])
+ names(df_data) <- c("id",paste0(key,c("$SEQUENCE")))
+ }
+ df_data <- convert_range_to_node(df_data, tree)
+ data_left[["node"]] <- df_merge(data_left[["node"]], df_data)
+ data_left[["tip"]] <- df_merge(data_left[["tip"]], df_data)
+ profile$name <- key
+ specific_themes$alignment$reference$ids <- 0
+ specific_themes$alignment$reference$use <- 0
+ specific_themes$alignment$reference$box_border_width <- 0
+ specific_themes$alignment$reference$box_border_color <- ""
+ specific_themes$alignment$reference$box_fill_color <- ""
+ specific_themes$alignment$highlight$type <- ""
+ unit <- new("itol.unit", type = type, sep = sep, profile = profile, field = field, common_themes = common_themes, specific_themes = specific_themes, data = data_left)
+ }
if(type=="DATASET_CONNECTION"){
if(!is.data.frame(data)){
stop("The input data class should be a data frame")
@@ -1394,8 +1541,8 @@ create_unit <- function(data,key,type,style="default",subtype=NULL,color=NULL,li
color = "table2itol"
}
if(length(color) == 1){
- if(color %in% c("table2itol","RColorBrewer", "ggsci")){
- color_levels = get_color(length(unique(data[[colname_data]])))
+ if(stringr::str_remove(color,"_.*$") %in% get_color(set="ls")){
+ color_levels = get_color(length(unique(data[[colname_data]])),set = color)
color = as.factor(data[[colname_data]])
levels(color) <- color_levels
}else {
@@ -1423,8 +1570,137 @@ create_unit <- function(data,key,type,style="default",subtype=NULL,color=NULL,li
sep = "\t"
unit <- new("itol.unit", type = type, sep = sep, profile = profile, field = field, common_themes = common_themes, specific_themes = specific_themes, data = data_left)
}
- if(type =="DATASET_IMAGE"){
-
+ if(type =="DATASET_IMAGE"){#ID,position,size_factor,rotation,horizontal_shift,vertical_shift,image_url
+ horizontal_shift = NULL
+ vertical_shift = NULL
+ if(!is.data.frame(data)){
+ stop("The input data class should be a data frame")
+ }
+ if(names(data)[1] != "id"){
+ message(paste0("Using the first column as id: ",names(data)[1]))
+ names(data)[1] <- "id"
+ }
+ if(length(names(data)) > 7 ){
+ stop("The input data should has 2-7 columns: id, position(optional), size factor(optional), rotation(optional), horizontal shift(optional), vertical shift(optional), image url")
+ }
+ colname_position = ""
+ if(is.null(position)){
+ potential_positions <- names(data)[-1]
+ for (potential_position in potential_positions) {
+ if(stringr::str_remove_all(paste0(data[[potential_position]],collapse = ""),"[\\d\\.-]") == "" && stringr::str_count(paste0(data[[potential_position]],collapse = ""),"\\.") <= 1){
+ potential_values <- as.numeric(data[[potential_position]])
+ if(all((potential_values >= -1) & (potential_values <= 1))){
+ message(paste0("Using following column as position parameter: ", potential_position))
+ position = data[[potential_position]]
+ colname_position = potential_position
+ break
+ }
+ }
+ }
+ }
+ colname_image_size = ""
+ if(is.null(size_factor)){
+ potential_image_sizes <- names(data)[!names(data)%in%c("id", colname_position)]
+ for (potential_image_size in potential_image_sizes) {
+ if(stringr::str_remove_all(paste0(data[[potential_image_size]],collapse = ""),"[\\d\\.-]") == "" && stringr::str_count(paste0(data[[potential_image_size]],collapse = ""),"\\.") <= 1){
+ message(paste0("Using following column as image size parameter: ", potential_image_size))
+ size_factor = data[[potential_image_size]]
+ colname_image_size = potential_image_size
+ break
+ }
+ }
+ }
+ colname_rotation = ""
+ if(is.null(rotation)){
+ potential_rotations <- names(data)[!names(data)%in%c("id", colname_position, colname_image_size)]
+ for (potential_rotation in potential_rotations) {
+ if(stringr::str_remove_all(paste0(data[[potential_rotation]],collapse = ""),"[\\d\\.-]") == "" && stringr::str_count(paste0(data[[potential_rotation]],collapse = ""),"\\.") <= 1){
+ message(paste0("Using following column as rotation parameter: ", potential_rotation))
+ rotation = data[[potential_rotation]]
+ colname_rotation = potential_rotation
+ break
+ }
+ }
+ }
+ colname_horizontal_shift = ""
+ if(is.null(horizontal_shift)){
+ potential_horizontal_shifts <- names(data)[!names(data)%in%c("id", colname_position, colname_image_size, colname_rotation)]
+ for (potential_horizontal_shift in potential_horizontal_shifts) {
+ if(stringr::str_remove_all(paste0(data[[potential_horizontal_shift]],collapse = ""),"[\\d\\.-]") == "" && stringr::str_count(paste0(data[[potential_horizontal_shift]],collapse = ""),"\\.") <= 1){
+ message(paste0("Using following column as horizontal_shift parameter: ", potential_horizontal_shift))
+ horizontal_shift = data[[potential_horizontal_shift]]
+ colname_horizontal_shift = potential_horizontal_shift
+ break
+ }
+ }
+ }
+ colname_vertical_shift = ""
+ if(is.null(vertical_shift)){
+ potential_vertical_shifts <- names(data)[!names(data)%in%c("id", colname_position, colname_image_size, colname_rotation, colname_horizontal_shift)]
+ for (potential_vertical_shift in potential_vertical_shifts) {
+ if(stringr::str_remove_all(paste0(data[[potential_vertical_shift]],collapse = ""),"[\\d\\.-]") == "" && stringr::str_count(paste0(data[[potential_vertical_shift]],collapse = ""),"\\.") <= 1){
+ message(paste0("Using following column as vertical_shift parameter: ", potential_vertical_shift))
+ vertical_shift = data[[potential_vertical_shift]]
+ colname_vertical_shift = potential_vertical_shift
+ break
+ }
+ }
+ }
+ colname_image_url <- names(data)[!names(data)%in%c("id", colname_position, colname_image_size, colname_rotation, colname_horizontal_shift, colname_vertical_shift)]
+ if(is.null(position)){
+ message("The position parameter is empty. Using 0 as position.")
+ position = 0
+ }
+ if (is.null(size_factor)) {
+ message("The image size parameter is empty. Using 1 as image size.")
+ size_factor = 1
+ }
+ if(is.null(rotation)){
+ message("The rotation parameter is empty. Using 0 as rotation.")
+ rotation = 0
+ }
+ if (is.null(horizontal_shift)) {
+ message("The horizontal_shift parameter is empty. Using 0.")
+ horizontal_shift = "0"
+ }
+ if (is.null(vertical_shift)) {
+ message("The vertical_shift parameter is empty. Using 0.")
+ vertical_shift = "0"
+ }
+ df_data <- data.frame(id = data[["id"]], position = position, size_factor = size_factor, rotation = rotation, horizontal_shift = horizontal_shift, vertical_shift = vertical_shift, image_url = data[[colname_image_url]])
+ names(df_data) <- c("id",paste0(key,"$",c("POSITION", "SIZE_FACTOR", "ROTATION", "HORIZONTAL_SHIFT", "VERTICAL_SHIFT", "IMAGE_URL")))
+ df_data <- convert_range_to_node(df_data, tree)
+ data_left[["node"]] <- df_merge(data_left[["node"]], df_data)
+ data_left[["tip"]] <- df_merge(data_left[["tip"]], df_data)
+ profile$name <- key
+ unit <- new("itol.unit", type = type, sep = sep, profile = profile, field = field, common_themes = common_themes, specific_themes = specific_themes, data = data_left)
+ }
+ if(type=="POPUP_INFO"){#NODE_ID,POPUP_TITLE,POPUP_CONTENT
+ if(!is.data.frame(data)){
+ stop("The input data class should be a data frame")
+ }
+ if(names(data)[1] != "id"){
+ message(paste0("Using the 1st column as id: ",names(data)[1]))
+ names(data)[1] <- "id"
+ }
+ if(length(names(data)) != 3 ){
+ stop("The input data should has 3 columns: id, title, content")
+ }
+ if(names(data)[2] != "title"){
+ message(paste0("Using the 2nd column as title: ",names(data)[2]))
+ names(data)[2] <- "title"
+ }
+ if(names(data)[3] != "content"){
+ message(paste0("Using the 3rd column as content: ",names(data)[3]))
+ names(data)[3] <- "content"
+ }
+ df_data <- data.frame(id = data[["id"]], title = data[["title"]], content = data[["content"]])
+ names(df_data) <- c("id",paste0(key,"$",c("POPUP_TITLE", "POPUP_CONTENT")))
+ df_data <- convert_range_to_node(df_data, tree)
+ data_left[["node"]] <- df_merge(data_left[["node"]], df_data)
+ data_left[["tip"]] <- df_merge(data_left[["tip"]], df_data)
+ profile$name <- key
+ unit <- new("itol.unit", type = type, sep = sep, profile = profile, field = field, common_themes = common_themes, specific_themes = specific_themes, data = data_left)
}
return(unit)
}
diff --git a/R/utils.R b/R/utils.R
index 5944d9e..eaf9fa2 100644
--- 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
index 25d4f4a..bad40d4 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -32,7 +32,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
index 5afa91f..1df5564 100644
--- a/docs/CODE_OF_CONDUCT.html
+++ b/docs/CODE_OF_CONDUCT.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index aa00016..d13ab44 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
index 3617178..37b331a 100644
--- a/docs/LICENSE.html
+++ b/docs/LICENSE.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/articles/Get_Start.html b/docs/articles/Get_Start.html
index b8557a9..b58f3e0 100644
--- a/docs/articles/Get_Start.html
+++ b/docs/articles/Get_Start.html
@@ -33,7 +33,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 35529e7..cee6fce 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/authors.html b/docs/authors.html
index b404e9e..0959e37 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
@@ -64,13 +64,13 @@ Citation
Zhou T (2023).
itol.toolkit: Helper Functions for 'Interactive Tree Of Life'.
-R package version 1.0.5.
+R package version 1.1.0.
@Manual{,
title = {itol.toolkit: Helper Functions for 'Interactive Tree Of Life'},
author = {Tong Zhou},
year = {2023},
- note = {R package version 1.0.5},
+ note = {R package version 1.1.0},
}
diff --git a/docs/index.html b/docs/index.html
index 7ff5aff..17c1adf 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -36,7 +36,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 95b01a1..5b90b15 100644
--- 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
index a60d0d2..0776e28 100644
--- a/docs/reference/complex_html_text.html
+++ b/docs/reference/complex_html_text.html
@@ -18,7 +18,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/reference/convert_01.html b/docs/reference/convert_01.html
index b5c1865..007fb7b 100644
--- a/docs/reference/convert_01.html
+++ b/docs/reference/convert_01.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/reference/convert_01_to_connect.html b/docs/reference/convert_01_to_connect.html
index 89c6aef..cf85810 100644
--- a/docs/reference/convert_01_to_connect.html
+++ b/docs/reference/convert_01_to_connect.html
@@ -18,7 +18,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/reference/convert_range_to_node.html b/docs/reference/convert_range_to_node.html
index 6d6e68a..4785a45 100644
--- a/docs/reference/convert_range_to_node.html
+++ b/docs/reference/convert_range_to_node.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/reference/correct_get_color.html b/docs/reference/correct_get_color.html
index a418708..53511a6 100644
--- a/docs/reference/correct_get_color.html
+++ b/docs/reference/correct_get_color.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/reference/count_to_tree.html b/docs/reference/count_to_tree.html
index e4a2f40..d7224ad 100644
--- a/docs/reference/count_to_tree.html
+++ b/docs/reference/count_to_tree.html
@@ -21,7 +21,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/reference/create_hub.html b/docs/reference/create_hub.html
index 9e2d50c..80f46a4 100644
--- a/docs/reference/create_hub.html
+++ b/docs/reference/create_hub.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/reference/create_theme.html b/docs/reference/create_theme.html
index 68bf441..e20dd52 100644
--- a/docs/reference/create_theme.html
+++ b/docs/reference/create_theme.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/reference/create_unit.html b/docs/reference/create_unit.html
index b707402..5076cdd 100644
--- a/docs/reference/create_unit.html
+++ b/docs/reference/create_unit.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/reference/df_merge.html b/docs/reference/df_merge.html
index fd5619a..a533717 100644
--- a/docs/reference/df_merge.html
+++ b/docs/reference/df_merge.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/reference/fa_read.html b/docs/reference/fa_read.html
index 3c9cd44..734eb0f 100644
--- a/docs/reference/fa_read.html
+++ b/docs/reference/fa_read.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/reference/fa_write.html b/docs/reference/fa_write.html
index 487bdfd..c818e9d 100644
--- a/docs/reference/fa_write.html
+++ b/docs/reference/fa_write.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/reference/file_get_dir.html b/docs/reference/file_get_dir.html
index c003686..c72c030 100644
--- a/docs/reference/file_get_dir.html
+++ b/docs/reference/file_get_dir.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/reference/file_get_name.html b/docs/reference/file_get_name.html
index 9ac79be..5bb77d3 100644
--- a/docs/reference/file_get_name.html
+++ b/docs/reference/file_get_name.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/reference/file_to_unit.html b/docs/reference/file_to_unit.html
index 0c92dba..991da11 100644
--- a/docs/reference/file_to_unit.html
+++ b/docs/reference/file_to_unit.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
diff --git a/docs/reference/get_color.html b/docs/reference/get_color.html
index 5145464..fadc5d0 100644
--- a/docs/reference/get_color.html
+++ b/docs/reference/get_color.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0
@@ -54,7 +54,7 @@ get_color
-
get_color(n, set = "table2itol")
+
get_color(n = 0, set = "table2itol")
diff --git a/docs/reference/head_line.html b/docs/reference/head_line.html
index ef5ca6c..c03dd1f 100644
--- a/docs/reference/head_line.html
+++ b/docs/reference/head_line.html
@@ -17,7 +17,7 @@
itol.toolkit
- 1.0.5
+ 1.1.0