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v1.1.10

Tong Zhou

2025-09-01

v1.1.10.Rmd

Overview

Updates:

  1. New: Correcting the spelling of the type parameter.
  2. Update: Beautifying the loading prompt format.
  3. Update: Fixing the SHOW_VALUE output parameter for the simplebar unit.

1. Correcting the Spelling of the type Parameter

This feature can be used to simplify the process and reduce error rates. For example, with DATASET_COLORSTRIP, it supports partial input, case insensitivity, and recognition of misspellings.

## 
## ── Loading ────────────────────────────────────────────── itol.toolkit 1.1.11 ──
## 
## If you use the itol.toolkit package in published research, please cite:
## 
## Zhou, T., Xu, K., Zhao, F., Liu, W., Li, L., Hua, Z., & Zhou, X. (2023).
## itol.toolkit accelerates working with iTOL (Interactive Tree of Life) by an
## automated generation of annotation files. Bioinformatics, 39(6), btad339.
# read data
tree <- system.file("extdata",
                    "tree_of_itol_templates.tree",
                    package = "itol.toolkit")
data("template_groups")
df_group <- data.frame(id = unique(template_groups$group), 
                       data = unique(template_groups$group))

# 1. Partial input "COLORSTRIP" can be correctly recognized
unit <- create_unit(data = df_group, 
                    key = "Quickstart", 
                    type = "COLORSTRIP", 
                    tree = tree)
## Using default color pattern: table2itol
# [1] "DATASET_COLORSTRIP"

# 2. Partial input "STRIP" can be correctly recognized
unit <- create_unit(data = df_group, 
                    key = "Quickstart", 
                    type = "STRIP", 
                    tree = tree)
## Using default color pattern: table2itol
# [1] "DATASET_COLORSTRIP"

# 3. Lowercase input "strip" can be correctly recognized
unit <- create_unit(data = df_group, 
                    key = "Quickstart", 
                    type = "strip", 
                    tree = tree)
## Using default color pattern: table2itol
# [1] "DATASET_COLORSTRIP"

# 4. Misspelled input "strib" can be correctly recognized
unit <- create_unit(data = df_group, 
                    key = "Quickstart", 
                    type = "strib", 
                    tree = tree)
## Using default color pattern: table2itol
# [1] "DATASET_COLORSTRIP"

2. Optimizing Loading Prompts

The previous loading prompts were red, which could mislead users into thinking there was an error. Therefore, the font color has been optimized, but the content still serves as a reminder to properly cite the papers.

# You can try running it to see the actual effect
library(itol.toolkit)
# ── Loading ───────────────────────────────────────── itol.toolkit 1.1.9 ──
#
# If you use the itol.toolkit package in published research, please cite:
#
# Zhou, T., Xu, K., Zhao, F., Liu, W., Li, L., Hua, Z., & Zhou, X. (2023).
# itol.toolkit accelerates working with iTOL (Interactive Tree of Life) by an
# automated generation of annotation files. Bioinformatics, 39(6), btad339.

3. Correcting the SHOW_VALUE Output for Simplebar

An issue was identified during the creation of the DATASET_SIMPLEBAR unit, where the output parameter for value_display was incorrectly set to SHOW_VALUES instead of SHOW_VALUE. Setting unit_3@specific_themes$basic_plot$value_display <- 1 previously generated the field SHOW_VALUES 1, but the iTOL web template requires SHOW_VALUE 1. The extra “S” in the field name prevented the setting from being properly recognized. After reviewing the show_value setting across all templates, it was confirmed that only DATASET_SIMPLEBAR requires SHOW_VALUE, while other templates continue to use SHOW_VALUES.