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:

The geological timescale data is based on the ICS International Chronostratigraphic Chart 2023/02 (https://stratigraphy.org/chart/).