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
#> ============================================================
#> 2026-11-03T00:50:53.806+08:00 | INFO     | Starting plot_timetree pipeline
#> 2026-11-03T00:50:53.806+08:00 | INFO     | Tree input               : phylo object
#> 2026-11-03T00:50:53.806+08:00 | INFO     | Rank                     : phylum
#> 2026-11-03T00:50:53.807+08:00 | INFO     | Layout                   : rectangular
#> 2026-11-03T00:50:53.808+08:00 | INFO     | Unit                     : auto
#> 2026-11-03T00:50:53.808+08:00 | INFO     | Step 1/7: Input validation and reading
#> 
#>   --------------------------------------------------
#>   >> Input Validation
#>   --------------------------------------------------
#> 2026-11-03T00:50:53.810+08:00 | INFO     | Tips                     : 50
#> 2026-11-03T00:50:53.811+08:00 | INFO     | Internal nodes           : 49
#> 2026-11-03T00:50:53.811+08:00 | INFO     | Edge lengths range       : 40.1579 to 2758.4006
#> 2026-11-03T00:50:53.812+08:00 | INFO     | Input validation passed
#> 2026-11-03T00:50:53.812+08:00 | INFO     | Timer 'input_reading': 4 ms
#> 2026-11-03T00:50:53.812+08:00 | INFO     | Step 2/7: Taxonomy parsing
#> 2026-11-03T00:50:53.812+08:00 | INFO     | Using rank-based taxonomy: phylum
#> 2026-11-03T00:50:54.199+08:00 | INFO     | Detected format          : GTDB
#> 2026-11-03T00:50:54.199+08:00 | INFO     | Groups found             : 5
#> 2026-11-03T00:50:54.199+08:00 | INFO     | Timer 'taxonomy_parsing': 387 ms
#> 2026-11-03T00:50:54.200+08:00 | INFO     | Step 3/7: MRCA computation and monophyly check
#> 2026-11-03T00:50:54.200+08:00 | INFO     | Checking monophyly and computing MRCA for each group...
#> 2026-11-03T00:50:54.203+08:00 | INFO     | Valid groups for collapse: 5 out of 5 total groups
#> 2026-11-03T00:50:54.203+08:00 | INFO     | Valid MRCA nodes         : 5
#> 2026-11-03T00:50:54.203+08:00 | INFO     | Timer 'mrca_computation': 4 ms
#> 2026-11-03T00:50:54.808+08:00 | INFO     | Step 4/7: Color generation
#> 2026-11-03T00:50:54.878+08:00 | INFO     | Color palette            : viridis
#> 2026-11-03T00:50:54.879+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.
#> 2026-11-03T00:50:54.983+08:00 | INFO     | Collapsing 5 clades...
#> 2026-11-03T00:50:55.010+08:00 | INFO     | Clade collapse complete
#> 2026-11-03T00:50:55.011+08:00 | INFO     | Timer 'tree_rendering': 132 ms
#> 2026-11-03T00:50:55.011+08:00 | INFO     | Step 6/7: Timescale integration
#> 
#> ============================================================
#>                       Pipeline Complete
#> ============================================================
#> 2026-11-03T00:50:55.272+08:00 | INFO     |   Tips                        : 50
#> 2026-11-03T00:50:55.272+08:00 | INFO     |   Groups parsed               : 5
#> 2026-11-03T00:50:55.272+08:00 | INFO     |   Groups collapsed            : 5
#> 2026-11-03T00:50:55.272+08:00 | INFO     |   Singleton groups            : 0
#> 2026-11-03T00:50:55.273+08:00 | INFO     |   Skipped (non-monophyletic)  : 0
#> 2026-11-03T00:50:55.273+08:00 | INFO     |   Skipped (root/zero-tip)     : 0
#> 2026-11-03T00:50:55.273+08:00 | INFO     |   Taxonomy format             : GTDB
#> 2026-11-03T00:50:55.273+08:00 | INFO     |   Layout                      : rectangular
#> 2026-11-03T00:50:55.273+08:00 | INFO     |   Timescale                   : disabled
#> 2026-11-03T00:50:55.273+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
#> ============================================================
#> 2026-11-03T00:50:55.633+08:00 | INFO     | Starting plot_timetree pipeline
#> 2026-11-03T00:50:55.633+08:00 | INFO     | Tree input               : phylo object
#> 2026-11-03T00:50:55.633+08:00 | INFO     | Rank                     : phylum
#> 2026-11-03T00:50:55.633+08:00 | INFO     | Layout                   : rectangular
#> 2026-11-03T00:50:55.633+08:00 | INFO     | Unit                     : auto
#> 2026-11-03T00:50:55.634+08:00 | INFO     | Step 1/7: Input validation and reading
#> 
#>   --------------------------------------------------
#>   >> Input Validation
#>   --------------------------------------------------
#> 2026-11-03T00:50:55.635+08:00 | INFO     | Tips                     : 50
#> 2026-11-03T00:50:55.635+08:00 | INFO     | Internal nodes           : 49
#> 2026-11-03T00:50:55.635+08:00 | INFO     | Edge lengths range       : 40.1579 to 2758.4006
#> 2026-11-03T00:50:55.636+08:00 | INFO     | Input validation passed
#> 2026-11-03T00:50:55.636+08:00 | INFO     | Timer 'input_reading': 1 ms
#> 2026-11-03T00:50:55.636+08:00 | INFO     | Step 2/7: Taxonomy parsing
#> 2026-11-03T00:50:55.636+08:00 | INFO     | Using rank-based taxonomy: phylum
#> 2026-11-03T00:50:55.646+08:00 | INFO     | Detected format          : GTDB
#> 2026-11-03T00:50:55.646+08:00 | INFO     | Groups found             : 5
#> 2026-11-03T00:50:55.647+08:00 | INFO     | Timer 'taxonomy_parsing': 10 ms
#> 2026-11-03T00:50:55.647+08:00 | INFO     | Step 3/7: MRCA computation and monophyly check
#> 2026-11-03T00:50:55.647+08:00 | INFO     | Checking monophyly and computing MRCA for each group...
#> 2026-11-03T00:50:55.648+08:00 | INFO     | Valid groups for collapse: 5 out of 5 total groups
#> 2026-11-03T00:50:55.648+08:00 | INFO     | Valid MRCA nodes         : 5
#> 2026-11-03T00:50:55.648+08:00 | INFO     | Timer 'mrca_computation': 1 ms
#> 2026-11-03T00:50:55.648+08:00 | INFO     | Step 4/7: Color generation
#> 2026-11-03T00:50:55.677+08:00 | INFO     | Color palette            : viridis
#> 2026-11-03T00:50:55.677+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.
#> 2026-11-03T00:50:55.730+08:00 | INFO     | Collapsing 5 clades...
#> 2026-11-03T00:50:55.772+08:00 | INFO     | Clade collapse complete
#> 2026-11-03T00:50:55.772+08:00 | INFO     | Timer 'tree_rendering': 95 ms
#> 2026-11-03T00:50:55.773+08:00 | INFO     | Step 6/7: Timescale integration
#> 
#> ============================================================
#>                       Pipeline Complete
#> ============================================================
#> 2026-11-03T00:50:55.816+08:00 | INFO     |   Tips                        : 50
#> 2026-11-03T00:50:55.816+08:00 | INFO     |   Groups parsed               : 5
#> 2026-11-03T00:50:55.816+08:00 | INFO     |   Groups collapsed            : 5
#> 2026-11-03T00:50:55.816+08:00 | INFO     |   Singleton groups            : 0
#> 2026-11-03T00:50:55.816+08:00 | INFO     |   Skipped (non-monophyletic)  : 0
#> 2026-11-03T00:50:55.816+08:00 | INFO     |   Skipped (root/zero-tip)     : 0
#> 2026-11-03T00:50:55.817+08:00 | INFO     |   Taxonomy format             : GTDB
#> 2026-11-03T00:50:55.817+08:00 | INFO     |   Layout                      : rectangular
#> 2026-11-03T00:50:55.817+08:00 | INFO     |   Timescale                   : disabled
#> 2026-11-03T00:50:55.818+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
#> ============================================================
#> 2026-11-03T00:50:56.090+08:00 | INFO     | Starting plot_timetree pipeline
#> 2026-11-03T00:50:56.091+08:00 | INFO     | Tree input               : phylo object
#> 2026-11-03T00:50:56.091+08:00 | INFO     | Rank                     : phylum
#> 2026-11-03T00:50:56.091+08:00 | INFO     | Layout                   : rectangular
#> 2026-11-03T00:50:56.091+08:00 | INFO     | Unit                     : auto
#> 2026-11-03T00:50:56.091+08:00 | INFO     | Step 1/7: Input validation and reading
#> 
#>   --------------------------------------------------
#>   >> Input Validation
#>   --------------------------------------------------
#> 2026-11-03T00:50:56.091+08:00 | INFO     | Tips                     : 50
#> 2026-11-03T00:50:56.092+08:00 | INFO     | Internal nodes           : 49
#> 2026-11-03T00:50:56.092+08:00 | INFO     | Edge lengths range       : 40.1579 to 2758.4006
#> 2026-11-03T00:50:56.093+08:00 | INFO     | Input validation passed
#> 2026-11-03T00:50:56.093+08:00 | INFO     | Timer 'input_reading': 2 ms
#> 2026-11-03T00:50:56.093+08:00 | INFO     | Step 2/7: Taxonomy parsing
#> 2026-11-03T00:50:56.093+08:00 | INFO     | Using rank-based taxonomy: phylum
#> 2026-11-03T00:50:56.097+08:00 | INFO     | Detected format          : GTDB
#> 2026-11-03T00:50:56.097+08:00 | INFO     | Groups found             : 5
#> 2026-11-03T00:50:56.097+08:00 | INFO     | Timer 'taxonomy_parsing': 4 ms
#> 2026-11-03T00:50:56.097+08:00 | INFO     | Step 3/7: MRCA computation and monophyly check
#> 2026-11-03T00:50:56.097+08:00 | INFO     | Checking monophyly and computing MRCA for each group...
#> 2026-11-03T00:50:56.098+08:00 | INFO     | Valid groups for collapse: 5 out of 5 total groups
#> 2026-11-03T00:50:56.099+08:00 | INFO     | Valid MRCA nodes         : 5
#> 2026-11-03T00:50:56.099+08:00 | INFO     | Timer 'mrca_computation': 1 ms
#> 2026-11-03T00:50:56.099+08:00 | INFO     | Step 4/7: Color generation
#> 2026-11-03T00:50:56.099+08:00 | INFO     | Color palette            : viridis
#> 2026-11-03T00:50:56.100+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.
#> 2026-11-03T00:50:56.155+08:00 | INFO     | Collapsing 5 clades...
#> 2026-11-03T00:50:56.170+08:00 | INFO     | Clade collapse complete
#> 2026-11-03T00:50:56.170+08:00 | INFO     | Timer 'tree_rendering': 70 ms
#> 2026-11-03T00:50:56.170+08:00 | INFO     | Step 6/7: Timescale integration
#> 
#> ============================================================
#>                       Pipeline Complete
#> ============================================================
#> 2026-11-03T00:50:56.224+08:00 | INFO     |   Tips                        : 50
#> 2026-11-03T00:50:56.224+08:00 | INFO     |   Groups parsed               : 5
#> 2026-11-03T00:50:56.225+08:00 | INFO     |   Groups collapsed            : 5
#> 2026-11-03T00:50:56.226+08:00 | INFO     |   Singleton groups            : 0
#> 2026-11-03T00:50:56.227+08:00 | INFO     |   Skipped (non-monophyletic)  : 0
#> 2026-11-03T00:50:56.227+08:00 | INFO     |   Skipped (root/zero-tip)     : 0
#> 2026-11-03T00:50:56.227+08:00 | INFO     |   Taxonomy format             : GTDB
#> 2026-11-03T00:50:56.227+08:00 | INFO     |   Layout                      : rectangular
#> 2026-11-03T00:50:56.227+08:00 | INFO     |   Timescale                   : disabled
#> 2026-11-03T00:50:56.227+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
#> ============================================================
#> 2026-11-03T00:50:56.228+08:00 | INFO     | Starting plot_timetree pipeline
#> 2026-11-03T00:50:56.228+08:00 | INFO     | Tree input               : phylo object
#> 2026-11-03T00:50:56.228+08:00 | INFO     | Rank                     : phylum
#> 2026-11-03T00:50:56.229+08:00 | INFO     | Layout                   : rectangular
#> 2026-11-03T00:50:56.229+08:00 | INFO     | Unit                     : auto
#> 2026-11-03T00:50:56.229+08:00 | INFO     | Step 1/7: Input validation and reading
#> 
#>   --------------------------------------------------
#>   >> Input Validation
#>   --------------------------------------------------
#> 2026-11-03T00:50:56.230+08:00 | INFO     | Tips                     : 50
#> 2026-11-03T00:50:56.230+08:00 | INFO     | Internal nodes           : 49
#> 2026-11-03T00:50:56.231+08:00 | INFO     | Edge lengths range       : 40.1579 to 2758.4006
#> 2026-11-03T00:50:56.231+08:00 | INFO     | Input validation passed
#> 2026-11-03T00:50:56.231+08:00 | INFO     | Timer 'input_reading': 2 ms
#> 2026-11-03T00:50:56.232+08:00 | INFO     | Step 2/7: Taxonomy parsing
#> 2026-11-03T00:50:56.232+08:00 | INFO     | Using rank-based taxonomy: phylum
#> 2026-11-03T00:50:56.241+08:00 | INFO     | Detected format          : GTDB
#> 2026-11-03T00:50:56.243+08:00 | INFO     | Groups found             : 5
#> 2026-11-03T00:50:56.243+08:00 | INFO     | Timer 'taxonomy_parsing': 11 ms
#> 2026-11-03T00:50:56.244+08:00 | INFO     | Step 3/7: MRCA computation and monophyly check
#> 2026-11-03T00:50:56.244+08:00 | INFO     | Checking monophyly and computing MRCA for each group...
#> 2026-11-03T00:50:56.246+08:00 | INFO     | Valid groups for collapse: 5 out of 5 total groups
#> 2026-11-03T00:50:56.246+08:00 | INFO     | Valid MRCA nodes         : 5
#> 2026-11-03T00:50:56.246+08:00 | INFO     | Timer 'mrca_computation': 2 ms
#> 2026-11-03T00:50:56.246+08:00 | INFO     | Step 4/7: Color generation
#> 2026-11-03T00:50:56.247+08:00 | INFO     | Color palette            : viridis
#> 2026-11-03T00:50:56.247+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.
#> 2026-11-03T00:50:56.292+08:00 | INFO     | Collapsing 5 clades...
#> 2026-11-03T00:50:56.311+08:00 | INFO     | Clade collapse complete
#> 2026-11-03T00:50:56.312+08:00 | INFO     | Timer 'tree_rendering': 64 ms
#> 2026-11-03T00:50:56.312+08:00 | INFO     | Step 6/7: Timescale integration
#> 
#> ============================================================
#>                       Pipeline Complete
#> ============================================================
#> 2026-11-03T00:50:56.346+08:00 | INFO     |   Tips                        : 50
#> 2026-11-03T00:50:56.346+08:00 | INFO     |   Groups parsed               : 5
#> 2026-11-03T00:50:56.346+08:00 | INFO     |   Groups collapsed            : 5
#> 2026-11-03T00:50:56.346+08:00 | INFO     |   Singleton groups            : 0
#> 2026-11-03T00:50:56.346+08:00 | INFO     |   Skipped (non-monophyletic)  : 0
#> 2026-11-03T00:50:56.346+08:00 | INFO     |   Skipped (root/zero-tip)     : 0
#> 2026-11-03T00:50:56.346+08:00 | INFO     |   Taxonomy format             : GTDB
#> 2026-11-03T00:50:56.346+08:00 | INFO     |   Layout                      : rectangular
#> 2026-11-03T00:50:56.347+08:00 | INFO     |   Timescale                   : disabled
#> 2026-11-03T00:50:56.347+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
#> ============================================================
#> 2026-11-03T00:50:56.395+08:00 | INFO     | Starting plot_timetree pipeline
#> 2026-11-03T00:50:56.395+08:00 | INFO     | Tree input               : phylo object
#> 2026-11-03T00:50:56.395+08:00 | INFO     | Rank                     : phylum
#> 2026-11-03T00:50:56.396+08:00 | INFO     | Layout                   : rectangular
#> 2026-11-03T00:50:56.396+08:00 | INFO     | Unit                     : auto
#> 2026-11-03T00:50:56.396+08:00 | INFO     | Step 1/7: Input validation and reading
#> 
#>   --------------------------------------------------
#>   >> Input Validation
#>   --------------------------------------------------
#> 2026-11-03T00:50:56.396+08:00 | INFO     | Tips                     : 50
#> 2026-11-03T00:50:56.396+08:00 | INFO     | Internal nodes           : 49
#> 2026-11-03T00:50:56.396+08:00 | INFO     | Edge lengths range       : 40.1579 to 2758.4006
#> 2026-11-03T00:50:56.397+08:00 | INFO     | Input validation passed
#> 2026-11-03T00:50:56.397+08:00 | INFO     | Timer 'input_reading': 1 ms
#> 2026-11-03T00:50:56.397+08:00 | INFO     | Step 2/7: Taxonomy parsing
#> 2026-11-03T00:50:56.397+08:00 | INFO     | Using rank-based taxonomy: phylum
#> 2026-11-03T00:50:56.402+08:00 | INFO     | Detected format          : GTDB
#> 2026-11-03T00:50:56.402+08:00 | INFO     | Groups found             : 5
#> 2026-11-03T00:50:56.402+08:00 | INFO     | Timer 'taxonomy_parsing': 5 ms
#> 2026-11-03T00:50:56.403+08:00 | INFO     | Step 3/7: MRCA computation and monophyly check
#> 2026-11-03T00:50:56.403+08:00 | INFO     | Checking monophyly and computing MRCA for each group...
#> 2026-11-03T00:50:56.403+08:00 | INFO     | Valid groups for collapse: 5 out of 5 total groups
#> 2026-11-03T00:50:56.404+08:00 | INFO     | Valid MRCA nodes         : 5
#> 2026-11-03T00:50:56.404+08:00 | INFO     | Timer 'mrca_computation': 1 ms
#> 2026-11-03T00:50:56.404+08:00 | INFO     | Step 4/7: Color generation
#> 2026-11-03T00:50:56.404+08:00 | INFO     | Color palette            : viridis
#> 2026-11-03T00:50:56.405+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.
#> 2026-11-03T00:50:56.449+08:00 | INFO     | Collapsing 5 clades...
#> 2026-11-03T00:50:56.463+08:00 | INFO     | Clade collapse complete
#> 2026-11-03T00:50:56.463+08:00 | INFO     | Timer 'tree_rendering': 58 ms
#> 2026-11-03T00:50:56.464+08:00 | INFO     | Step 6/7: Timescale integration
#> 
#> ============================================================
#>                       Pipeline Complete
#> ============================================================
#> 2026-11-03T00:50:56.506+08:00 | INFO     |   Tips                        : 50
#> 2026-11-03T00:50:56.506+08:00 | INFO     |   Groups parsed               : 5
#> 2026-11-03T00:50:56.506+08:00 | INFO     |   Groups collapsed            : 5
#> 2026-11-03T00:50:56.507+08:00 | INFO     |   Singleton groups            : 0
#> 2026-11-03T00:50:56.507+08:00 | INFO     |   Skipped (non-monophyletic)  : 0
#> 2026-11-03T00:50:56.507+08:00 | INFO     |   Skipped (root/zero-tip)     : 0
#> 2026-11-03T00:50:56.507+08:00 | INFO     |   Taxonomy format             : GTDB
#> 2026-11-03T00:50:56.507+08:00 | INFO     |   Layout                      : rectangular
#> 2026-11-03T00:50:56.507+08:00 | INFO     |   Timescale                   : disabled
#> 2026-11-03T00:50:56.507+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/).