Text alignment & 20+ colors

[TongZhou2017]

DOI: 10.1016:j.jhazmat.2022.129230
Status: with tree and template files
Location: Fig2
Elements:
Fig2

10.1016:j.jhazmat.2022.129230.zip

[TongZhou2017]

library(itol.toolkit)
library(data.table) 
library(ape) 
library(stringr) 

tree <- "tree.nwk" 
phylo <- ape::read.tree(tree)
phylo$tip.label <- stringr::str_remove(phylo$tip.label, "_.*$") 
tree <- "tree_short_label.nwk"
ape::write.tree(phylo,tree) 

hub <- create_hub(tree)

data_file <- "iTOL_annotation.txt"
data <- data.table::fread(data_file)
data <- data %>% filter(ID != "Seq30_")

select_tip = phylo$tip.label[phylo$tip.label != "Seq372"]
unit_1 <- create_unit(data = select_tip, 
                                 key = "rep_Li2022jhm_1_prune", 
                                 type = "PRUNE", 
                                 tree = tree)

df_gene <- data %>% select(ID, Gene_name)
unit_2 <- create_unit(data = df_gene, 
                                 key = "rep_Li2022jhm_4_text_1", 
                                 type = "DATASET_TEXT", 
                                 size_factor = 1,
                                 rotation= 180,
                                 position = -1,
                                 color = "#000000",
                                 tree = tree)
unit_2@common_themes$basic_theme$margin <- -500

df_relabel <- data %>% select(ID, Substrate)
unit_3 <- create_unit(data = df_relabel, 
                      key = "rep_Li2022jhm_2_labels", 
                      type = "LABELS",
                      tree = tree)

df_substrate <- data %>% select(ID, Substrate)
set.seed(666)
unit_4 <- create_unit(data = df_substrate, 
                    key = "rep_Li2022jhm_3_range", 
                    type = "TREE_COLORS", 
                    subtype = "range", 
                    color = "wesanderson",
                    tree = tree)

df_species <- data %>% select(ID, Species)
unit_5 <- create_unit(data = df_species, 
                                 key = "rep_Li2022jhm_5_text_2", 
                                 type = "DATASET_TEXT", 
                                 size_factor = 1,
                                 rotation= 0,
                                 position = -1,
                                 color ="#000000",
                                 tree = tree)
unit_5@common_themes$basic_theme$margin <- 50

hub <- hub + unit_1 + unit_2 + unit_3 + unit_4 + unit_5
write_hub(hub, getwd())