A complete dataset should include at least the following:
Tree file in Newick format.
Metadata.
Metadata files for most functions should be comma seperated files or
table seperated files that could be imported into R by
data.table. Only a few function has its own special
metadata format (e.g. DATASET_ALIGNMENT)
data.table::fread to read metadata
metadata_path <-system.file("extdata","parameter_groups.txt",package = "itol.toolkit")
meta_data <- data.table::fread(metadata_path)ape::read.tree to read the tree file. If it is a non-phylo
object tree calculated in the R environment, it is recommended to use
ape::as.phylo to convert it to a phylo object.
tree_path <- system.file("extdata","tree_of_itol_templates.tree",package = "itol.toolkit")
tree <- read.tree(tree_path)Users will get unit or hub object after
itol.toolkit annotation. You can use write_unit to output a
single unit object, and the output content will be the
template file corresponding to the object’s type attribute. Also, you
can add multiple units to the hub object, and then use
write_hub to output the template file in bulk.
To fully demonstrate itol.toolkit functions, we
presented five datasets:
iTOL parameter structure and usage. This is a very small dataset, mainly used for the most basic function demonstration.
Li_2022_JHazardMater. This is a multi group dataset that focuses on text display, mainly used for displaying TEXT functions and palette systems.
Zheng_2022_EnvironPollut. This includes a small phylogenetic tree, a large phylogenetic tree, and a comprehensive dataset for multi-dimensional data comparison. It is mainly used for palette display, browser overload testing, and demonstrate the comprehensive use of multiple functions.
Zhou_2022_FoodRes. This is a dataset mainly used for comparing with table2itol.
Tree of life. This is an official standard dataset from iTOL, mainly used for demonstrating how to extract and combine metadata from existing templates.
| Name | Import inside R | GitHub url | Note |
|---|---|---|---|
| Tree file | system.file("extdata","tree_of_itol_templates.tree",package = "itol.toolkit") |
itol_templates.tree | Newick format，branches are 23 template names，nodes are 5 template types |
| Metadata1 raw parameter table | system.file("extdata","parameter_groups.txt",package = "itol.toolkit") |
parameter_usage_raw.txt | Tab seperated file，parameters are on row，template names are on column |
| Metadata2 parameter table | data("template_parameters_count") |
parameter_usage_count.txt | Tab seperated file，parameters are on row，template names are on column，converted from parameter_usage_raw.txt |
| Metadata3 frequency table | system.file("extdata","templates_frequence.txt",package = "itol.toolkit") |
templates_frequence.txt | Tab seperated file，template names are on row，DOIs are on column |
| Metadata4 classification | data("template_groups") |
template_groups.txt | Tab seperated file，the first column is template name，the second column is template type |
| Name | GitHub url | Note |
|---|---|---|
| Tree file | tree.nwk | Newick format，branches are 104 OTU IDs |
| Metadata | metadata.txt | Tab seperated file, the first column is sequence id，the second column is unused data，the third column is gene name，the fourth column is substrate，the fifth column is species name |
| Name | GitHub url | Note |
|---|---|---|
| Tree file1 Subtree | abunt-tree.nwk | Newick format，branches are 39 OTU IDs |
| Metadata1 Species and their abundance | abunt-metadata.txt | Tab seperated file, the first column is OTU ID, the second column is NS group abundance, the third column is OS group abundance, the fourth column is phylum, the fifth column is class, the sixth column is species, the sixth column is indicators with differences |
| Tree file2 Whole tree | rare-tree.nwk | Newick format，branches are 1338 OTU IDs |
| Metadata2 Species and their abundance | rare-metadata.txt | Tab seperated file, the first column is OTU ID, the second column is NS group abundance, the third column is OS group abundance, the fourth column is phylum, the fifth column is class, the sixth column is species, the sixth column is indicators with differences |
| Tree file3 iCAMP bin tree | assembly-tree.nwk | Newick format，branches are bins |
| Metadata3 iCAMP result | assembly-metadata.txt | Tab seperated file, the first column is bin ID, others are iCAMP output results |
| Name | GitHub url | Note |
|---|---|---|
| Tree file | otus.contree | Newick format，branches are 186 ASV IDs |
| Metadata | annotation.txt | Tab seperated file, the first column is ASV id，the 2-8 columns are taxonomy name in different level，the 9th column is total abundance，the 10-12 columns are abundance in different sample |
See iTOL offical example data here.
CACMS, njbxhzy@hotmail.com↩︎
IOCAS, tongzhou2017@gmail.com↩︎