itol.toolkit (version 1.1.7)

write_raw: Write raw data into files

Description

Write raw data in itol.hub object into files

Usage

write_raw(object, dir, title)

Value

No return value, only output raw data files

Arguments

object

itol.hub object holds the complete data and theme information. This is an all-in-one object that collects all the information. Based on this object, it is possible to export template files directly. It can also be converted to an operation unit object for the detailed processing of individual datasets. The object can also be saved locally for reproducible visualization to share. This object contains species or sample clustering trees, sequence alignment, species abundance or gene expression table, multi-level taxonomic information, metadata, and a list of custom themes. Each element name in the theme list is prefixed with the column name of the metadata and is used to establish the association between the theme and the data. For some special dataset types, the storage location is not in the metadata, but it also conforms to the association with themes. The program automatically decides where to read the data according to the different output template types. The user only needs to explicitly define the theme name to be output consistent with the data name prefix.

dir

output dir path. Define the output files location using absolute or relative path. The raw data will write into files. The following raw data will be outputted: main tree, sample tree, alignment sequences, abundance count table, taxonomy table, metadata on nodes and tips.

title

files name title string. This character specified the prefix of raw data files.

Examples

tree <- system.file("extdata",
                    "tree_of_itol_templates.tree",
                    package = "itol.toolkit")
hub <- create_hub(tree = tree)
df_values <- data.table::fread(system.file("extdata",
                                           "templates_frequence.txt",
                                           package = "itol.toolkit"))
unit <- create_unit(data = df_values,
                    key = "Quickstart",
                    type = "DATASET_HEATMAP",
                    tree = tree)
hub <- hub + unit
write_raw(hub,tempdir(),"Quickstart")