use.theme {itol.toolkit}

Extract theme from inbuilt_themes

Description

Extract theme from 23 template types in inbuilt_themes data in package.

Usage

use.theme(type, style = "default")

Arguments

type

a character specifying the template type used for extracting. Following choices are possible: "COLLAPSE","PRUNE","SPACING","TREE_COLORS", "DATASET_STYLE","LABELS","DATASET_TEXT","DATASET_COLORSTRIP", "DATASET_BINARY","DATASET_GRADIENT","DATASET_HEATMAP","DATASET_SYMBOL", "DATASET_EXTERNALSHAPE","DATASET_DOMAINS","DATASET_SIMPLEBAR", "DATASET_MULTIBAR","DATASET_BOXPLOT","DATASET_LINECHART","DATASET_PIECHART", "DATASET_ALIGNMENT","DATASET_CONNECTION","DATASET_IMAGE","POPUP_INFO.

style

a character specifying the specific version of template type used for extracting. The default value is "default" style for all types.

Value

a itol.theme object containing

type

This group holds information about the template type of the data only. This is a very critical piece of information. In many functions of the itol.toolkit package, the template type information is used to determine the different data processing and input/output methods.

sep

This group holds data separator information only. This is one of the most important parameters for data reading and output. It is a separate category because it is frequently used and is an input parameter for other subsequent parameters to be read.

profile

This group contains basic information about the dataset, such as the dataset name and a color label to distinguish the dataset. The dataset name is extremely important. This parameter is used almost throughout the data processing of the itol.toolkit package. With the content of this parameter as the key value, the data and theme information of the dataset are associated. In turn, high throughput learning and writing of large-scale data can be achieved. This parameter is not included in some template types with a particularly simple structure, so we choose a file name or a user-defined method as the key value.

field

This group contains information about each sample within the dataset, and this type of parameter exists only for multi-sample data. This information even includes the clustering tree between samples. This information is usually stored as part of the column names in the metadata part or abundance information of the itol.hub object.

common_themes

These themes are used at high frequency in different templates. These parameters are small in number but constitute some common features of iTOL visual style settings, such as legend, margin, etc.

specific_themes

These themes are used only in specific templates. The number of these parameters is very large. However, most of them are used in only one template to control the style details of the visualization. By unifying these parameters and calling them according to the template type, users can perform secondary development and data processing with a high degree of parameter aggregation without worrying too much about the differences between different template types.

Examples

theme <- use.theme("COLLAPSE")