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Publication-Ready Output
Color-Blind Friendly Palettes
Rclade defaults to the viridis palette, which is: -
Color-blind friendly - Grayscale friendly - Perceptually uniform
library(Rclade)
data(example_tree)
# Default viridis palette
p <- plot_timetree(example_tree, rank = "phylum",
taxonomy_format = "GTDB",
add_timescale = FALSE)
#>
#> ============================================================
#> Rclade: Phylogenetic Tree Visualization
#> ============================================================
#> 2026-09-16T00:09:24.864+08:00 | INFO | Starting plot_timetree pipeline
#> 2026-09-16T00:09:24.864+08:00 | INFO | Tree input : phylo object
#> 2026-09-16T00:09:24.864+08:00 | INFO | Rank : phylum
#> 2026-09-16T00:09:24.864+08:00 | INFO | Layout : rectangular
#> 2026-09-16T00:09:24.864+08:00 | INFO | Unit : auto
#> 2026-09-16T00:09:24.865+08:00 | INFO | Step 1/7: Input validation and reading
#>
#> --------------------------------------------------
#> >> Input Validation
#> --------------------------------------------------
#> 2026-09-16T00:09:24.865+08:00 | INFO | Tips : 50
#> 2026-09-16T00:09:24.865+08:00 | INFO | Internal nodes : 49
#> 2026-09-16T00:09:24.865+08:00 | INFO | Edge lengths range : 40.1579 to 2758.4006
#> 2026-09-16T00:09:24.866+08:00 | INFO | Input validation passed
#> 2026-09-16T00:09:24.866+08:00 | INFO | Timer 'input_reading': 1 ms
#> 2026-09-16T00:09:24.866+08:00 | INFO | Step 2/7: Taxonomy parsing
#> 2026-09-16T00:09:24.866+08:00 | INFO | Using rank-based taxonomy: phylum
#> 2026-09-16T00:09:24.940+08:00 | INFO | Detected format : GTDB
#> 2026-09-16T00:09:24.941+08:00 | INFO | Groups found : 5
#> 2026-09-16T00:09:24.941+08:00 | INFO | Timer 'taxonomy_parsing': 75 ms
#> 2026-09-16T00:09:24.941+08:00 | INFO | Step 3/7: MRCA computation and monophyly check
#> 2026-09-16T00:09:24.941+08:00 | INFO | Checking monophyly and computing MRCA for each group...
#> 2026-09-16T00:09:24.943+08:00 | INFO | Valid groups for collapse: 5 out of 5 total groups
#> 2026-09-16T00:09:24.943+08:00 | INFO | Valid MRCA nodes : 5
#> 2026-09-16T00:09:24.943+08:00 | INFO | Timer 'mrca_computation': 2 ms
#> 2026-09-16T00:09:25.220+08:00 | INFO | Step 4/7: Color generation
#> 2026-09-16T00:09:25.277+08:00 | INFO | Color palette : viridis
#> 2026-09-16T00:09:25.277+08:00 | INFO | Step 5/7: Tree rendering
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> 2026-09-16T00:09:25.363+08:00 | INFO | Collapsing 5 clades...
#> 2026-09-16T00:09:25.379+08:00 | INFO | Clade collapse complete
#> 2026-09-16T00:09:25.380+08:00 | INFO | Timer 'tree_rendering': 102 ms
#> 2026-09-16T00:09:25.380+08:00 | INFO | Step 6/7: Timescale integration
#>
#> ============================================================
#> Pipeline Complete
#> ============================================================
#> 2026-09-16T00:09:25.527+08:00 | INFO | Tips : 50
#> 2026-09-16T00:09:25.527+08:00 | INFO | Groups parsed : 5
#> 2026-09-16T00:09:25.527+08:00 | INFO | Groups collapsed : 5
#> 2026-09-16T00:09:25.527+08:00 | INFO | Singleton groups : 0
#> 2026-09-16T00:09:25.527+08:00 | INFO | Skipped (non-monophyletic) : 0
#> 2026-09-16T00:09:25.527+08:00 | INFO | Skipped (root/zero-tip) : 0
#> 2026-09-16T00:09:25.527+08:00 | INFO | Taxonomy format : GTDB
#> 2026-09-16T00:09:25.527+08:00 | INFO | Layout : rectangular
#> 2026-09-16T00:09:25.528+08:00 | INFO | Timescale : disabled
#> 2026-09-16T00:09:25.528+08:00 | INFO | plot_timetree completed successfully
print(p)
Custom Color Mapping
# Custom color mapping for specific groups
p <- plot_timetree(example_tree, rank = "phylum",
taxonomy_format = "GTDB",
add_timescale = FALSE,
color_mapping = c("Proteobacteria" = "#E41A1C",
"Firmicutes" = "#377EB8"))
#>
#> ============================================================
#> Rclade: Phylogenetic Tree Visualization
#> ============================================================
#> 2026-09-16T00:09:25.809+08:00 | INFO | Starting plot_timetree pipeline
#> 2026-09-16T00:09:25.809+08:00 | INFO | Tree input : phylo object
#> 2026-09-16T00:09:25.809+08:00 | INFO | Rank : phylum
#> 2026-09-16T00:09:25.810+08:00 | INFO | Layout : rectangular
#> 2026-09-16T00:09:25.810+08:00 | INFO | Unit : auto
#> 2026-09-16T00:09:25.810+08:00 | INFO | Step 1/7: Input validation and reading
#>
#> --------------------------------------------------
#> >> Input Validation
#> --------------------------------------------------
#> 2026-09-16T00:09:25.810+08:00 | INFO | Tips : 50
#> 2026-09-16T00:09:25.810+08:00 | INFO | Internal nodes : 49
#> 2026-09-16T00:09:25.810+08:00 | INFO | Edge lengths range : 40.1579 to 2758.4006
#> 2026-09-16T00:09:25.811+08:00 | INFO | Input validation passed
#> 2026-09-16T00:09:25.811+08:00 | INFO | Timer 'input_reading': 1 ms
#> 2026-09-16T00:09:25.812+08:00 | INFO | Step 2/7: Taxonomy parsing
#> 2026-09-16T00:09:25.812+08:00 | INFO | Using rank-based taxonomy: phylum
#> 2026-09-16T00:09:25.819+08:00 | INFO | Detected format : GTDB
#> 2026-09-16T00:09:25.819+08:00 | INFO | Groups found : 5
#> 2026-09-16T00:09:25.820+08:00 | INFO | Timer 'taxonomy_parsing': 8 ms
#> 2026-09-16T00:09:25.820+08:00 | INFO | Step 3/7: MRCA computation and monophyly check
#> 2026-09-16T00:09:25.820+08:00 | INFO | Checking monophyly and computing MRCA for each group...
#> 2026-09-16T00:09:25.821+08:00 | INFO | Valid groups for collapse: 5 out of 5 total groups
#> 2026-09-16T00:09:25.821+08:00 | INFO | Valid MRCA nodes : 5
#> 2026-09-16T00:09:25.821+08:00 | INFO | Timer 'mrca_computation': 1 ms
#> 2026-09-16T00:09:25.821+08:00 | INFO | Step 4/7: Color generation
#> 2026-09-16T00:09:25.842+08:00 | INFO | Color palette : viridis
#> 2026-09-16T00:09:25.842+08:00 | INFO | Step 5/7: Tree rendering
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> 2026-09-16T00:09:25.884+08:00 | INFO | Collapsing 5 clades...
#> 2026-09-16T00:09:25.896+08:00 | INFO | Clade collapse complete
#> 2026-09-16T00:09:25.896+08:00 | INFO | Timer 'tree_rendering': 54 ms
#> 2026-09-16T00:09:25.896+08:00 | INFO | Step 6/7: Timescale integration
#>
#> ============================================================
#> Pipeline Complete
#> ============================================================
#> 2026-09-16T00:09:25.925+08:00 | INFO | Tips : 50
#> 2026-09-16T00:09:25.925+08:00 | INFO | Groups parsed : 5
#> 2026-09-16T00:09:25.926+08:00 | INFO | Groups collapsed : 5
#> 2026-09-16T00:09:25.926+08:00 | INFO | Singleton groups : 0
#> 2026-09-16T00:09:25.926+08:00 | INFO | Skipped (non-monophyletic) : 0
#> 2026-09-16T00:09:25.926+08:00 | INFO | Skipped (root/zero-tip) : 0
#> 2026-09-16T00:09:25.926+08:00 | INFO | Taxonomy format : GTDB
#> 2026-09-16T00:09:25.926+08:00 | INFO | Layout : rectangular
#> 2026-09-16T00:09:25.926+08:00 | INFO | Timescale : disabled
#> 2026-09-16T00:09:25.926+08:00 | INFO | plot_timetree completed successfully
print(p)
Legend Placement
# Inside the plot (default)
p <- plot_timetree(example_tree, rank = "phylum",
taxonomy_format = "GTDB",
add_timescale = FALSE,
legend_position = c(0.05, 0.85))
#>
#> ============================================================
#> Rclade: Phylogenetic Tree Visualization
#> ============================================================
#> 2026-09-16T00:09:26.154+08:00 | INFO | Starting plot_timetree pipeline
#> 2026-09-16T00:09:26.154+08:00 | INFO | Tree input : phylo object
#> 2026-09-16T00:09:26.155+08:00 | INFO | Rank : phylum
#> 2026-09-16T00:09:26.155+08:00 | INFO | Layout : rectangular
#> 2026-09-16T00:09:26.155+08:00 | INFO | Unit : auto
#> 2026-09-16T00:09:26.155+08:00 | INFO | Step 1/7: Input validation and reading
#>
#> --------------------------------------------------
#> >> Input Validation
#> --------------------------------------------------
#> 2026-09-16T00:09:26.155+08:00 | INFO | Tips : 50
#> 2026-09-16T00:09:26.155+08:00 | INFO | Internal nodes : 49
#> 2026-09-16T00:09:26.155+08:00 | INFO | Edge lengths range : 40.1579 to 2758.4006
#> 2026-09-16T00:09:26.156+08:00 | INFO | Input validation passed
#> 2026-09-16T00:09:26.156+08:00 | INFO | Timer 'input_reading': 1 ms
#> 2026-09-16T00:09:26.156+08:00 | INFO | Step 2/7: Taxonomy parsing
#> 2026-09-16T00:09:26.156+08:00 | INFO | Using rank-based taxonomy: phylum
#> 2026-09-16T00:09:26.160+08:00 | INFO | Detected format : GTDB
#> 2026-09-16T00:09:26.160+08:00 | INFO | Groups found : 5
#> 2026-09-16T00:09:26.160+08:00 | INFO | Timer 'taxonomy_parsing': 4 ms
#> 2026-09-16T00:09:26.160+08:00 | INFO | Step 3/7: MRCA computation and monophyly check
#> 2026-09-16T00:09:26.160+08:00 | INFO | Checking monophyly and computing MRCA for each group...
#> 2026-09-16T00:09:26.161+08:00 | INFO | Valid groups for collapse: 5 out of 5 total groups
#> 2026-09-16T00:09:26.161+08:00 | INFO | Valid MRCA nodes : 5
#> 2026-09-16T00:09:26.161+08:00 | INFO | Timer 'mrca_computation': 1 ms
#> 2026-09-16T00:09:26.161+08:00 | INFO | Step 4/7: Color generation
#> 2026-09-16T00:09:26.162+08:00 | INFO | Color palette : viridis
#> 2026-09-16T00:09:26.162+08:00 | INFO | Step 5/7: Tree rendering
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> 2026-09-16T00:09:26.201+08:00 | INFO | Collapsing 5 clades...
#> 2026-09-16T00:09:26.212+08:00 | INFO | Clade collapse complete
#> 2026-09-16T00:09:26.212+08:00 | INFO | Timer 'tree_rendering': 50 ms
#> 2026-09-16T00:09:26.212+08:00 | INFO | Step 6/7: Timescale integration
#>
#> ============================================================
#> Pipeline Complete
#> ============================================================
#> 2026-09-16T00:09:26.240+08:00 | INFO | Tips : 50
#> 2026-09-16T00:09:26.240+08:00 | INFO | Groups parsed : 5
#> 2026-09-16T00:09:26.240+08:00 | INFO | Groups collapsed : 5
#> 2026-09-16T00:09:26.240+08:00 | INFO | Singleton groups : 0
#> 2026-09-16T00:09:26.240+08:00 | INFO | Skipped (non-monophyletic) : 0
#> 2026-09-16T00:09:26.240+08:00 | INFO | Skipped (root/zero-tip) : 0
#> 2026-09-16T00:09:26.240+08:00 | INFO | Taxonomy format : GTDB
#> 2026-09-16T00:09:26.240+08:00 | INFO | Layout : rectangular
#> 2026-09-16T00:09:26.240+08:00 | INFO | Timescale : disabled
#> 2026-09-16T00:09:26.240+08:00 | INFO | plot_timetree completed successfully
# Standard positions
p <- plot_timetree(example_tree, rank = "phylum",
taxonomy_format = "GTDB",
add_timescale = FALSE,
legend_position = "right")
#>
#> ============================================================
#> Rclade: Phylogenetic Tree Visualization
#> ============================================================
#> 2026-09-16T00:09:26.241+08:00 | INFO | Starting plot_timetree pipeline
#> 2026-09-16T00:09:26.241+08:00 | INFO | Tree input : phylo object
#> 2026-09-16T00:09:26.241+08:00 | INFO | Rank : phylum
#> 2026-09-16T00:09:26.241+08:00 | INFO | Layout : rectangular
#> 2026-09-16T00:09:26.241+08:00 | INFO | Unit : auto
#> 2026-09-16T00:09:26.241+08:00 | INFO | Step 1/7: Input validation and reading
#>
#> --------------------------------------------------
#> >> Input Validation
#> --------------------------------------------------
#> 2026-09-16T00:09:26.242+08:00 | INFO | Tips : 50
#> 2026-09-16T00:09:26.242+08:00 | INFO | Internal nodes : 49
#> 2026-09-16T00:09:26.242+08:00 | INFO | Edge lengths range : 40.1579 to 2758.4006
#> 2026-09-16T00:09:26.242+08:00 | INFO | Input validation passed
#> 2026-09-16T00:09:26.242+08:00 | INFO | Timer 'input_reading': 1 ms
#> 2026-09-16T00:09:26.242+08:00 | INFO | Step 2/7: Taxonomy parsing
#> 2026-09-16T00:09:26.243+08:00 | INFO | Using rank-based taxonomy: phylum
#> 2026-09-16T00:09:26.246+08:00 | INFO | Detected format : GTDB
#> 2026-09-16T00:09:26.247+08:00 | INFO | Groups found : 5
#> 2026-09-16T00:09:26.247+08:00 | INFO | Timer 'taxonomy_parsing': 4 ms
#> 2026-09-16T00:09:26.247+08:00 | INFO | Step 3/7: MRCA computation and monophyly check
#> 2026-09-16T00:09:26.247+08:00 | INFO | Checking monophyly and computing MRCA for each group...
#> 2026-09-16T00:09:26.248+08:00 | INFO | Valid groups for collapse: 5 out of 5 total groups
#> 2026-09-16T00:09:26.248+08:00 | INFO | Valid MRCA nodes : 5
#> 2026-09-16T00:09:26.248+08:00 | INFO | Timer 'mrca_computation': 1 ms
#> 2026-09-16T00:09:26.248+08:00 | INFO | Step 4/7: Color generation
#> 2026-09-16T00:09:26.249+08:00 | INFO | Color palette : viridis
#> 2026-09-16T00:09:26.249+08:00 | INFO | Step 5/7: Tree rendering
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> 2026-09-16T00:09:26.285+08:00 | INFO | Collapsing 5 clades...
#> 2026-09-16T00:09:26.299+08:00 | INFO | Clade collapse complete
#> 2026-09-16T00:09:26.299+08:00 | INFO | Timer 'tree_rendering': 50 ms
#> 2026-09-16T00:09:26.300+08:00 | INFO | Step 6/7: Timescale integration
#>
#> ============================================================
#> Pipeline Complete
#> ============================================================
#> 2026-09-16T00:09:26.328+08:00 | INFO | Tips : 50
#> 2026-09-16T00:09:26.329+08:00 | INFO | Groups parsed : 5
#> 2026-09-16T00:09:26.329+08:00 | INFO | Groups collapsed : 5
#> 2026-09-16T00:09:26.329+08:00 | INFO | Singleton groups : 0
#> 2026-09-16T00:09:26.329+08:00 | INFO | Skipped (non-monophyletic) : 0
#> 2026-09-16T00:09:26.329+08:00 | INFO | Skipped (root/zero-tip) : 0
#> 2026-09-16T00:09:26.329+08:00 | INFO | Taxonomy format : GTDB
#> 2026-09-16T00:09:26.329+08:00 | INFO | Layout : rectangular
#> 2026-09-16T00:09:26.329+08:00 | INFO | Timescale : disabled
#> 2026-09-16T00:09:26.329+08:00 | INFO | plot_timetree completed successfully
Clade Labels
p <- plot_timetree(example_tree, rank = "phylum",
taxonomy_format = "GTDB",
add_timescale = FALSE,
show_clade_label = TRUE)
#>
#> ============================================================
#> Rclade: Phylogenetic Tree Visualization
#> ============================================================
#> 2026-09-16T00:09:26.366+08:00 | INFO | Starting plot_timetree pipeline
#> 2026-09-16T00:09:26.366+08:00 | INFO | Tree input : phylo object
#> 2026-09-16T00:09:26.366+08:00 | INFO | Rank : phylum
#> 2026-09-16T00:09:26.366+08:00 | INFO | Layout : rectangular
#> 2026-09-16T00:09:26.366+08:00 | INFO | Unit : auto
#> 2026-09-16T00:09:26.366+08:00 | INFO | Step 1/7: Input validation and reading
#>
#> --------------------------------------------------
#> >> Input Validation
#> --------------------------------------------------
#> 2026-09-16T00:09:26.367+08:00 | INFO | Tips : 50
#> 2026-09-16T00:09:26.367+08:00 | INFO | Internal nodes : 49
#> 2026-09-16T00:09:26.367+08:00 | INFO | Edge lengths range : 40.1579 to 2758.4006
#> 2026-09-16T00:09:26.367+08:00 | INFO | Input validation passed
#> 2026-09-16T00:09:26.368+08:00 | INFO | Timer 'input_reading': 1 ms
#> 2026-09-16T00:09:26.368+08:00 | INFO | Step 2/7: Taxonomy parsing
#> 2026-09-16T00:09:26.368+08:00 | INFO | Using rank-based taxonomy: phylum
#> 2026-09-16T00:09:26.372+08:00 | INFO | Detected format : GTDB
#> 2026-09-16T00:09:26.372+08:00 | INFO | Groups found : 5
#> 2026-09-16T00:09:26.372+08:00 | INFO | Timer 'taxonomy_parsing': 4 ms
#> 2026-09-16T00:09:26.372+08:00 | INFO | Step 3/7: MRCA computation and monophyly check
#> 2026-09-16T00:09:26.372+08:00 | INFO | Checking monophyly and computing MRCA for each group...
#> 2026-09-16T00:09:26.373+08:00 | INFO | Valid groups for collapse: 5 out of 5 total groups
#> 2026-09-16T00:09:26.373+08:00 | INFO | Valid MRCA nodes : 5
#> 2026-09-16T00:09:26.373+08:00 | INFO | Timer 'mrca_computation': 1 ms
#> 2026-09-16T00:09:26.374+08:00 | INFO | Step 4/7: Color generation
#> 2026-09-16T00:09:26.374+08:00 | INFO | Color palette : viridis
#> 2026-09-16T00:09:26.374+08:00 | INFO | Step 5/7: Tree rendering
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> 2026-09-16T00:09:26.411+08:00 | INFO | Collapsing 5 clades...
#> 2026-09-16T00:09:26.423+08:00 | INFO | Clade collapse complete
#> 2026-09-16T00:09:26.423+08:00 | INFO | Timer 'tree_rendering': 49 ms
#> 2026-09-16T00:09:26.424+08:00 | INFO | Step 6/7: Timescale integration
#>
#> ============================================================
#> Pipeline Complete
#> ============================================================
#> 2026-09-16T00:09:26.457+08:00 | INFO | Tips : 50
#> 2026-09-16T00:09:26.457+08:00 | INFO | Groups parsed : 5
#> 2026-09-16T00:09:26.457+08:00 | INFO | Groups collapsed : 5
#> 2026-09-16T00:09:26.457+08:00 | INFO | Singleton groups : 0
#> 2026-09-16T00:09:26.457+08:00 | INFO | Skipped (non-monophyletic) : 0
#> 2026-09-16T00:09:26.457+08:00 | INFO | Skipped (root/zero-tip) : 0
#> 2026-09-16T00:09:26.457+08:00 | INFO | Taxonomy format : GTDB
#> 2026-09-16T00:09:26.458+08:00 | INFO | Layout : rectangular
#> 2026-09-16T00:09:26.458+08:00 | INFO | Timescale : disabled
#> 2026-09-16T00:09:26.458+08:00 | INFO | plot_timetree completed successfully
print(p)
Taxonomy Quality Report
Before finalizing your figure, verify label parsing quality:
summarize_taxonomy_quality(example_tree$tip.label, format = "GTDB")
#> === Taxonomy Label Parsing Quality Report ===
#> Total labels: 50
#> Detected format: GTDB
#>
#> Per-rank parse rates:
#> kingdom 0.0% (0/50)
#> domain 100.0% (50/50) ====================
#> phylum 100.0% (50/50) ====================
#> class 100.0% (50/50) ====================
#> order 0.0% (0/50)
#> family 0.0% (0/50)
#> genus 0.0% (0/50)
#> species 0.0% (0/50)
#> subspecies 0.0% (0/50)
#>
#> All labels parsed successfully.
Batch Processing
Process multiple tree files at once:
batch_plot(input_dir = "trees/",
output_dir = "figures/",
pattern = "*.tre",
rank = "phylum",
taxonomy_format = "GTDB")
Reproducibility
save_session_info("session_info.txt")
References & Acknowledgments
Rclade builds on the ggtree and
deeptime R packages. If you use Rclade in published
research, please cite Rclade along with these key dependencies:
- Yu G, Smith DK, Zhu H, Guan Y, Lam TT-Y (2017). “ggtree: an R
package for visualization and annotation of phylogenetic trees with
their covariates and other associated data.” Methods in Ecology and
Evolution, 8(1), 28-36. doi:10.1111/2041-210X.12628
- Gearty W (2025). “deeptime: an R package that facilitates highly
customizable and reproducible visualizations of data over geological
time intervals.” Big Earth Data. doi:10.1080/20964471.2025.2537516
The geological timescale data is based on the ICS International
Chronostratigraphic Chart 2023/02 (https://stratigraphy.org/chart/).
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.