itol.toolkit (version 1.1.7)

create_unit: Create itol.unit

Description

Create itol.unit from simple input in R environment.

Usage

create_unit(
  data,
  key,
  type,
  style = "default",
  subtype = NULL,
  color = NULL,
  line_type = NULL,
  font_type = NULL,
  size_factor = NULL,
  position = NULL,
  background_color = NULL,
  rotation = NULL,
  method = NULL,
  shape = NULL,
  fill = NULL,
  tree
)

Value

a itol.unit 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.

data

This slot contains a list of two data frames with the nodes and tips data separately. The first column of the two data frames is the node or tip id. If the input data contains range id, it would be converted to node id by the convert_range_to_node function automatically.

Arguments

data

if type == "COLLAPSE", a vector of characters specifying the tips or node used for collapsing used for extracting.

key

a character specifying the output file name for hub object.

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.

subtype

a character specifying the subtype under type. If the type is "TREE_COLORS", the following choices are possible: "range", "clade", "branch", "label", "label_background".

color

a character specifying the color pattern name. The following choices are possible: "table2itol", "RColorBrewer", "ggsci".

line_type

a character specifying the normal or dashed line type used in clade and branch subtype.

font_type

a character specifying the bold, italic, and bold-italic font type used in label and branch subtype.

size_factor

a number specifying the line width used in clade and branch subtype and size factor in label subtype.

position

If type == "DATASET_STYLE", a character specifying the position: The following choices are possible: "node" and "clade". If type == "DATASET_TEXT", a number specifying the position of the text on the tree: -1 = external label; a number between 0 and 1 = internal label positioned at the specified value along the node branch (for example, position 0 is exactly at the start of node branch, position 0.5 is in the middle, and position 1 is at the end)

background_color

Only used while type == "DATASET_STYLE" and subtype == "label". a character or a vector of character specifying the background color in hexadecimal, RGB or RGBA notation.

rotation

Only used while type == "DATASET_TEXT". a number or a vector of number specifying the rotation angle of the text.

method

a character specifying the numbric data summarise method. If type == "DATASET_BINARY", the following choices are possible: "mean", "sum".

shape

a character or a vector of character specifying the symbol shape. If type == "DATASET_BINARY", the default is 2. If type == "DATASET_SYMBOL", the following choices are possible: 1 for rectangle, 2 for circle, 3 for star, 4 for left pointing triangle, 5 for right pointing triangle. If using NULL and there are data column, the functions will automaticly help users to setup the shapes based on the levels of the data.

fill

If type == "DATASET_SYMBOL", 1/0 is specifying the shape outlier filled or not. If type == "DATASET_DOMAINS", the following choices are possible: "RE|HH|HV|EL|DI|TR|TL|PL|PR|PU|PD|OC|GP".

tree

a character specifying Newick format tree file path or a phylo object of main phylogenetic tree.

Examples

tree <- system.file("extdata","tree_of_itol_templates.tree",package = "itol.toolkit")
data("template_groups")
data("template_parameters_count")
# COLLAPSE
group_names <- unique(template_groups$group)
object <- create_hub(tree = tree)
unit <- create_unit(data = group_names, key = "E001_collapse_1",
type = "COLLAPSE", tree = tree)
object <- learn_data_from_unit(object,unit)
# PRUNE
select_note = c("theme_style","basic_plot")
unit <- create_unit(data = select_note, key = "E002_prune_1",
type = "PRUNE", tree = tree)
object <- learn_data_from_unit(object,unit)
# SPACING
df_values = data.frame(id = row.names(template_parameters_count),
values = rowSums(template_parameters_count))
unit <- create_unit(data = df_values, key = "E005_spacing_1",
type = "SPACING", tree = tree)
object <- learn_data_from_unit(object,unit)
# TREE_COLORS
## range
unit <- create_unit(data = template_groups,
key = "E006_tree_colors_1", type = "TREE_COLORS", subtype = "range",
tree = tree)
object <- learn_data_from_unit(object,unit)