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
#> ============================================================
#> 2026-11-05T05:59:15.543+00:00 | INFO | Starting plot_timetree pipeline
#> 2026-11-05T05:59:15.544+00:00 | INFO | Tree input : phylo object
#> 2026-11-05T05:59:15.544+00:00 | INFO | Rank : phylum
#> 2026-11-05T05:59:15.544+00:00 | INFO | Layout : rectangular
#> 2026-11-05T05:59:15.545+00:00 | INFO | Unit : auto
#> 2026-11-05T05:59:15.545+00:00 | INFO | Step 1/7: Input validation and reading
#>
#> --------------------------------------------------
#> >> Input Validation
#> --------------------------------------------------
#> 2026-11-05T05:59:15.546+00:00 | INFO | Tips : 50
#> 2026-11-05T05:59:15.546+00:00 | INFO | Internal nodes : 49
#> 2026-11-05T05:59:15.547+00:00 | INFO | Edge lengths range : 40.1579 to 2758.4006
#> 2026-11-05T05:59:15.547+00:00 | INFO | Input validation passed
#> 2026-11-05T05:59:15.548+00:00 | INFO | Timer 'input_reading': 2 ms
#> 2026-11-05T05:59:15.548+00:00 | INFO | Step 2/7: Taxonomy parsing
#> 2026-11-05T05:59:15.549+00:00 | INFO | Using rank-based taxonomy: phylum
#> 2026-11-05T05:59:15.555+00:00 | INFO | Detected format : GTDB
#> 2026-11-05T05:59:15.555+00:00 | INFO | Groups found : 5
#> 2026-11-05T05:59:15.555+00:00 | INFO | Timer 'taxonomy_parsing': 7 ms
#> 2026-11-05T05:59:15.556+00:00 | INFO | Step 3/7: MRCA computation and monophyly check
#> 2026-11-05T05:59:15.556+00:00 | INFO | Checking monophyly and computing MRCA for each group...
#> 2026-11-05T05:59:15.559+00:00 | INFO | Valid groups for collapse: 5 out of 5 total groups
#> 2026-11-05T05:59:15.559+00:00 | INFO | Valid MRCA nodes : 5
#> 2026-11-05T05:59:15.559+00:00 | INFO | Timer 'mrca_computation': 4 ms
#> 2026-11-05T05:59:16.170+00:00 | INFO | Step 4/7: Color generation
#> 2026-11-05T05:59:16.175+00:00 | INFO | Color palette : viridis
#> 2026-11-05T05:59:16.175+00:00 | 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.
#> 2026-11-05T05:59:16.319+00:00 | INFO | Collapsing 5 clades...
#> 2026-11-05T05:59:16.343+00:00 | INFO | Clade collapse complete
#> 2026-11-05T05:59:16.343+00:00 | INFO | Timer 'tree_rendering': 167 ms
#> 2026-11-05T05:59:16.344+00:00 | INFO | Step 6/7: Timescale integration
#>
#> ============================================================
#> Pipeline Complete
#> ============================================================
#> 2026-11-05T05:59:16.417+00:00 | INFO | Tips : 50
#> 2026-11-05T05:59:16.418+00:00 | INFO | Groups parsed : 5
#> 2026-11-05T05:59:16.418+00:00 | INFO | Groups collapsed : 5
#> 2026-11-05T05:59:16.418+00:00 | INFO | Singleton groups : 0
#> 2026-11-05T05:59:16.418+00:00 | INFO | Skipped (non-monophyletic) : 0
#> 2026-11-05T05:59:16.419+00:00 | INFO | Skipped (root/zero-tip) : 0
#> 2026-11-05T05:59:16.419+00:00 | INFO | Taxonomy format : GTDB
#> 2026-11-05T05:59:16.419+00:00 | INFO | Layout : rectangular
#> 2026-11-05T05:59:16.420+00:00 | INFO | Timescale : disabled
#> 2026-11-05T05:59:16.420+00:00 | 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
#> ============================================================
#> 2026-11-05T05:59:16.979+00:00 | INFO | Starting plot_timetree pipeline
#> 2026-11-05T05:59:16.979+00:00 | INFO | Tree input : phylo object
#> 2026-11-05T05:59:16.980+00:00 | INFO | Rank : phylum
#> 2026-11-05T05:59:16.980+00:00 | INFO | Layout : rectangular
#> 2026-11-05T05:59:16.980+00:00 | INFO | Unit : auto
#> 2026-11-05T05:59:16.980+00:00 | INFO | Step 1/7: Input validation and reading
#>
#> --------------------------------------------------
#> >> Input Validation
#> --------------------------------------------------
#> 2026-11-05T05:59:16.981+00:00 | INFO | Tips : 50
#> 2026-11-05T05:59:16.981+00:00 | INFO | Internal nodes : 49
#> 2026-11-05T05:59:16.982+00:00 | INFO | Edge lengths range : 40.1579 to 2758.4006
#> 2026-11-05T05:59:16.982+00:00 | INFO | Input validation passed
#> 2026-11-05T05:59:16.983+00:00 | INFO | Timer 'input_reading': 2 ms
#> 2026-11-05T05:59:16.983+00:00 | INFO | Step 2/7: Taxonomy parsing
#> 2026-11-05T05:59:16.983+00:00 | INFO | Using rank-based taxonomy: phylum
#> 2026-11-05T05:59:16.988+00:00 | INFO | Detected format : GTDB
#> 2026-11-05T05:59:16.989+00:00 | INFO | Groups found : 5
#> 2026-11-05T05:59:16.989+00:00 | INFO | Timer 'taxonomy_parsing': 6 ms
#> 2026-11-05T05:59:16.989+00:00 | INFO | Step 3/7: MRCA computation and monophyly check
#> 2026-11-05T05:59:16.990+00:00 | INFO | Checking monophyly and computing MRCA for each group...
#> 2026-11-05T05:59:16.992+00:00 | INFO | Valid groups for collapse: 5 out of 5 total groups
#> 2026-11-05T05:59:16.992+00:00 | INFO | Valid MRCA nodes : 5
#> 2026-11-05T05:59:16.992+00:00 | INFO | Timer 'mrca_computation': 3 ms
#> 2026-11-05T05:59:16.993+00:00 | INFO | Step 4/7: Color generation
#> 2026-11-05T05:59:16.994+00:00 | INFO | Color palette : viridis
#> 2026-11-05T05:59:16.994+00:00 | 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.
#> 2026-11-05T05:59:17.084+00:00 | INFO | Collapsing 5 clades...
#> 2026-11-05T05:59:17.107+00:00 | INFO | Clade collapse complete
#> 2026-11-05T05:59:17.108+00:00 | INFO | Timer 'tree_rendering': 113 ms
#> 2026-11-05T05:59:17.108+00:00 | INFO | Step 6/7: Timescale integration
#>
#> ============================================================
#> Pipeline Complete
#> ============================================================
#> 2026-11-05T05:59:17.172+00:00 | INFO | Tips : 50
#> 2026-11-05T05:59:17.172+00:00 | INFO | Groups parsed : 5
#> 2026-11-05T05:59:17.173+00:00 | INFO | Groups collapsed : 5
#> 2026-11-05T05:59:17.173+00:00 | INFO | Singleton groups : 0
#> 2026-11-05T05:59:17.173+00:00 | INFO | Skipped (non-monophyletic) : 0
#> 2026-11-05T05:59:17.173+00:00 | INFO | Skipped (root/zero-tip) : 0
#> 2026-11-05T05:59:17.174+00:00 | INFO | Taxonomy format : GTDB
#> 2026-11-05T05:59:17.174+00:00 | INFO | Layout : rectangular
#> 2026-11-05T05:59:17.174+00:00 | INFO | Timescale : disabled
#> 2026-11-05T05:59:17.174+00:00 | 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
#> ============================================================
#> 2026-11-05T05:59:17.630+00:00 | INFO | Starting plot_timetree pipeline
#> 2026-11-05T05:59:17.630+00:00 | INFO | Tree input : phylo object
#> 2026-11-05T05:59:17.631+00:00 | INFO | Rank : phylum
#> 2026-11-05T05:59:17.631+00:00 | INFO | Layout : rectangular
#> 2026-11-05T05:59:17.631+00:00 | INFO | Unit : auto
#> 2026-11-05T05:59:17.632+00:00 | INFO | Step 1/7: Input validation and reading
#>
#> --------------------------------------------------
#> >> Input Validation
#> --------------------------------------------------
#> 2026-11-05T05:59:17.632+00:00 | INFO | Tips : 50
#> 2026-11-05T05:59:17.633+00:00 | INFO | Internal nodes : 49
#> 2026-11-05T05:59:17.633+00:00 | INFO | Edge lengths range : 40.1579 to 2758.4006
#> 2026-11-05T05:59:17.634+00:00 | INFO | Input validation passed
#> 2026-11-05T05:59:17.634+00:00 | INFO | Timer 'input_reading': 2 ms
#> 2026-11-05T05:59:17.634+00:00 | INFO | Step 2/7: Taxonomy parsing
#> 2026-11-05T05:59:17.634+00:00 | INFO | Using rank-based taxonomy: phylum
#> 2026-11-05T05:59:17.640+00:00 | INFO | Detected format : GTDB
#> 2026-11-05T05:59:17.640+00:00 | INFO | Groups found : 5
#> 2026-11-05T05:59:17.641+00:00 | INFO | Timer 'taxonomy_parsing': 6 ms
#> 2026-11-05T05:59:17.641+00:00 | INFO | Step 3/7: MRCA computation and monophyly check
#> 2026-11-05T05:59:17.641+00:00 | INFO | Checking monophyly and computing MRCA for each group...
#> 2026-11-05T05:59:17.643+00:00 | INFO | Valid groups for collapse: 5 out of 5 total groups
#> 2026-11-05T05:59:17.644+00:00 | INFO | Valid MRCA nodes : 5
#> 2026-11-05T05:59:17.644+00:00 | INFO | Timer 'mrca_computation': 3 ms
#> 2026-11-05T05:59:17.645+00:00 | INFO | Step 4/7: Color generation
#> 2026-11-05T05:59:17.646+00:00 | INFO | Color palette : viridis
#> 2026-11-05T05:59:17.646+00:00 | 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.
#> 2026-11-05T05:59:17.739+00:00 | INFO | Collapsing 5 clades...
#> 2026-11-05T05:59:17.762+00:00 | INFO | Clade collapse complete
#> 2026-11-05T05:59:17.762+00:00 | INFO | Timer 'tree_rendering': 116 ms
#> 2026-11-05T05:59:17.763+00:00 | INFO | Step 6/7: Timescale integration
#>
#> ============================================================
#> Pipeline Complete
#> ============================================================
#> 2026-11-05T05:59:17.829+00:00 | INFO | Tips : 50
#> 2026-11-05T05:59:17.829+00:00 | INFO | Groups parsed : 5
#> 2026-11-05T05:59:17.830+00:00 | INFO | Groups collapsed : 5
#> 2026-11-05T05:59:17.830+00:00 | INFO | Singleton groups : 0
#> 2026-11-05T05:59:17.830+00:00 | INFO | Skipped (non-monophyletic) : 0
#> 2026-11-05T05:59:17.830+00:00 | INFO | Skipped (root/zero-tip) : 0
#> 2026-11-05T05:59:17.830+00:00 | INFO | Taxonomy format : GTDB
#> 2026-11-05T05:59:17.831+00:00 | INFO | Layout : rectangular
#> 2026-11-05T05:59:17.831+00:00 | INFO | Timescale : disabled
#> 2026-11-05T05:59:17.831+00:00 | 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
#> ============================================================
#> 2026-11-05T05:59:17.832+00:00 | INFO | Starting plot_timetree pipeline
#> 2026-11-05T05:59:17.832+00:00 | INFO | Tree input : phylo object
#> 2026-11-05T05:59:17.833+00:00 | INFO | Rank : phylum
#> 2026-11-05T05:59:17.833+00:00 | INFO | Layout : rectangular
#> 2026-11-05T05:59:17.833+00:00 | INFO | Unit : auto
#> 2026-11-05T05:59:17.833+00:00 | INFO | Step 1/7: Input validation and reading
#>
#> --------------------------------------------------
#> >> Input Validation
#> --------------------------------------------------
#> 2026-11-05T05:59:17.834+00:00 | INFO | Tips : 50
#> 2026-11-05T05:59:17.834+00:00 | INFO | Internal nodes : 49
#> 2026-11-05T05:59:17.834+00:00 | INFO | Edge lengths range : 40.1579 to 2758.4006
#> 2026-11-05T05:59:17.835+00:00 | INFO | Input validation passed
#> 2026-11-05T05:59:17.835+00:00 | INFO | Timer 'input_reading': 2 ms
#> 2026-11-05T05:59:17.836+00:00 | INFO | Step 2/7: Taxonomy parsing
#> 2026-11-05T05:59:17.836+00:00 | INFO | Using rank-based taxonomy: phylum
#> 2026-11-05T05:59:17.841+00:00 | INFO | Detected format : GTDB
#> 2026-11-05T05:59:17.841+00:00 | INFO | Groups found : 5
#> 2026-11-05T05:59:17.842+00:00 | INFO | Timer 'taxonomy_parsing': 6 ms
#> 2026-11-05T05:59:17.842+00:00 | INFO | Step 3/7: MRCA computation and monophyly check
#> 2026-11-05T05:59:17.842+00:00 | INFO | Checking monophyly and computing MRCA for each group...
#> 2026-11-05T05:59:17.844+00:00 | INFO | Valid groups for collapse: 5 out of 5 total groups
#> 2026-11-05T05:59:17.844+00:00 | INFO | Valid MRCA nodes : 5
#> 2026-11-05T05:59:17.845+00:00 | INFO | Timer 'mrca_computation': 3 ms
#> 2026-11-05T05:59:17.845+00:00 | INFO | Step 4/7: Color generation
#> 2026-11-05T05:59:17.846+00:00 | INFO | Color palette : viridis
#> 2026-11-05T05:59:17.847+00:00 | 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.
#> 2026-11-05T05:59:17.932+00:00 | INFO | Collapsing 5 clades...
#> 2026-11-05T05:59:17.954+00:00 | INFO | Clade collapse complete
#> 2026-11-05T05:59:17.954+00:00 | INFO | Timer 'tree_rendering': 107 ms
#> 2026-11-05T05:59:17.959+00:00 | INFO | Step 6/7: Timescale integration
#>
#> ============================================================
#> Pipeline Complete
#> ============================================================
#> 2026-11-05T05:59:18.018+00:00 | INFO | Tips : 50
#> 2026-11-05T05:59:18.018+00:00 | INFO | Groups parsed : 5
#> 2026-11-05T05:59:18.019+00:00 | INFO | Groups collapsed : 5
#> 2026-11-05T05:59:18.019+00:00 | INFO | Singleton groups : 0
#> 2026-11-05T05:59:18.019+00:00 | INFO | Skipped (non-monophyletic) : 0
#> 2026-11-05T05:59:18.019+00:00 | INFO | Skipped (root/zero-tip) : 0
#> 2026-11-05T05:59:18.020+00:00 | INFO | Taxonomy format : GTDB
#> 2026-11-05T05:59:18.020+00:00 | INFO | Layout : rectangular
#> 2026-11-05T05:59:18.020+00:00 | INFO | Timescale : disabled
#> 2026-11-05T05:59:18.020+00:00 | INFO | plot_timetree completed successfullyClade Labels
p <- plot_timetree(example_tree, rank = "phylum",
taxonomy_format = "GTDB",
add_timescale = FALSE,
show_clade_label = TRUE)
#>
#> ============================================================
#> Rclade: Phylogenetic Tree Visualization
#> ============================================================
#> 2026-11-05T05:59:18.111+00:00 | INFO | Starting plot_timetree pipeline
#> 2026-11-05T05:59:18.111+00:00 | INFO | Tree input : phylo object
#> 2026-11-05T05:59:18.112+00:00 | INFO | Rank : phylum
#> 2026-11-05T05:59:18.112+00:00 | INFO | Layout : rectangular
#> 2026-11-05T05:59:18.112+00:00 | INFO | Unit : auto
#> 2026-11-05T05:59:18.112+00:00 | INFO | Step 1/7: Input validation and reading
#>
#> --------------------------------------------------
#> >> Input Validation
#> --------------------------------------------------
#> 2026-11-05T05:59:18.113+00:00 | INFO | Tips : 50
#> 2026-11-05T05:59:18.113+00:00 | INFO | Internal nodes : 49
#> 2026-11-05T05:59:18.114+00:00 | INFO | Edge lengths range : 40.1579 to 2758.4006
#> 2026-11-05T05:59:18.114+00:00 | INFO | Input validation passed
#> 2026-11-05T05:59:18.115+00:00 | INFO | Timer 'input_reading': 2 ms
#> 2026-11-05T05:59:18.115+00:00 | INFO | Step 2/7: Taxonomy parsing
#> 2026-11-05T05:59:18.115+00:00 | INFO | Using rank-based taxonomy: phylum
#> 2026-11-05T05:59:18.121+00:00 | INFO | Detected format : GTDB
#> 2026-11-05T05:59:18.121+00:00 | INFO | Groups found : 5
#> 2026-11-05T05:59:18.122+00:00 | INFO | Timer 'taxonomy_parsing': 6 ms
#> 2026-11-05T05:59:18.122+00:00 | INFO | Step 3/7: MRCA computation and monophyly check
#> 2026-11-05T05:59:18.122+00:00 | INFO | Checking monophyly and computing MRCA for each group...
#> 2026-11-05T05:59:18.124+00:00 | INFO | Valid groups for collapse: 5 out of 5 total groups
#> 2026-11-05T05:59:18.124+00:00 | INFO | Valid MRCA nodes : 5
#> 2026-11-05T05:59:18.125+00:00 | INFO | Timer 'mrca_computation': 3 ms
#> 2026-11-05T05:59:18.125+00:00 | INFO | Step 4/7: Color generation
#> 2026-11-05T05:59:18.126+00:00 | INFO | Color palette : viridis
#> 2026-11-05T05:59:18.127+00:00 | 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.
#> 2026-11-05T05:59:18.217+00:00 | INFO | Collapsing 5 clades...
#> 2026-11-05T05:59:18.240+00:00 | INFO | Clade collapse complete
#> 2026-11-05T05:59:18.241+00:00 | INFO | Timer 'tree_rendering': 114 ms
#> 2026-11-05T05:59:18.243+00:00 | INFO | Step 6/7: Timescale integration
#>
#> ============================================================
#> Pipeline Complete
#> ============================================================
#> 2026-11-05T05:59:18.312+00:00 | INFO | Tips : 50
#> 2026-11-05T05:59:18.312+00:00 | INFO | Groups parsed : 5
#> 2026-11-05T05:59:18.313+00:00 | INFO | Groups collapsed : 5
#> 2026-11-05T05:59:18.313+00:00 | INFO | Singleton groups : 0
#> 2026-11-05T05:59:18.313+00:00 | INFO | Skipped (non-monophyletic) : 0
#> 2026-11-05T05:59:18.313+00:00 | INFO | Skipped (root/zero-tip) : 0
#> 2026-11-05T05:59:18.314+00:00 | INFO | Taxonomy format : GTDB
#> 2026-11-05T05:59:18.314+00:00 | INFO | Layout : rectangular
#> 2026-11-05T05:59:18.314+00:00 | INFO | Timescale : disabled
#> 2026-11-05T05:59:18.314+00:00 | 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/).