DATASET_SYMBOL

Introduction

The function of DATASET_SYMBOL is to display various symbol shapes directly on the branches of the tree. The DATASET_GRADIENT template belongs to the “Basic graphics” class (refer to the Class for detail information).

Users typically add symbols to branches of a tree by inputting the branch names or nodes, as well as specifying the symbol’s size, color, fill, and position.

This section describes how to use itol.toolkit to add symbols to branches of a tree. Without itol.toolkit, users have to set a lot of information manually, such as the size and the location of each symbol. The itol.toolkit automatically configures the size, shape, and color of symbols and adjust the size of all symbols globally.

Draw symbols

This section uses dataset 1 as an example to demonstrate adding symbols to branches of a tree based on metadata information. (refer to the Dataset for detail information)

Load data

The first step is to load the newick format tree file tree_of_itol_templates.tree and its corresponding metadata template_parameters_count and template_groups.

The following sample file template_parameters_count contains contains style parameters and data parameter information for the template type, with each column being a parameter. A value of 1 indicates that the template uses this parameter, while a value of 0 indicates that it is not used. And the sample file template_groups.txt is the category information for the template, the first column is the template name, and the second column is the category information.

The purpose of our data processing in this section is to display the number of parameters used by each template by adding symbols to the branches of the tree. The more parameters a template uses, the larger the symbol.

library(itol.toolkit)
library(data.table)
library(ape)
tree <- system.file("extdata",
                    "tree_of_itol_templates.tree",
                    package = "itol.toolkit")
data("template_groups")
data("template_parameters_count")
tree <- read.tree(tree)

We can use different symbols for different groups. The program will automatically identify and set different colors and symbol shapes based on group information in template_groups. When the number of groups exceeds 6, the program will use different colors shapes to distinguish different groups automatically.

template_parameters_count <- data.frame(template_parameters_count)
df_data <- cbind(template_groups,as.data.frame(rowSums(template_parameters_count)))
unit_30 <- create_unit(data = df_data,
                    key = "E030_symbol_1",
                    type = "DATASET_SYMBOL",
                    position = 1,
                    tree = tree)

We can use the “position” parameter to set the position where the symbol appears.Position should be a number between 0 and 1, specifying the ratio of the branch length where the center of the symbol should be positioned. Here, we set the position to 0.5 to place the symbol in the middle of the branch.

unit_31 <- create_unit(data = df_data,
                    key = "E031_symbol_2",
                    type = "DATASET_SYMBOL",
                    position = 0.5,
                    tree = tree)

We can determine whether the symbol is filled by changing the fill parameter. 0 represents a outlined symbol, and 1 represents a filled symbol.

unit_32 <- create_unit(data = df_data,
                    key = "E032_symbol_3",
                    type = "DATASET_SYMBOL",
                    position = 0.5,
                    tree = tree,
                    fill = 0)

Style modification

By modifying unit@specific_themes$basic_plot$size_max, we can adjust the maximum size of the symbol.

unit_32@specific_themes$basic_plot$size_max <- 40

Weiyue Liu1, Zhongyi Hua2, Tong Zhou3

Introduction

Draw symbols

Load data

Style modification

Weiyue Liu¹, Zhongyi Hua², Tong Zhou³