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Customizing Style in phylobar

Source: vignettes/customizing_files.Rmd
customizing_files.Rmd

Overview

Phylobar draws a phylogenetic tree alongside a stacked bar chart. This vignette shows how to customize visual style: text sizes, color palettes, layout ratios, legend placement, and more.

We will use a small random dataset:

library(ape)
library(phylobar)

set.seed(1)
tree <- rtree(20)
samples <- matrix(rpois(100 * 20, 1), nrow = 100, ncol = 20)

phylobar(samples, tree)

The function signature and key styling parameters we will explore:

  • palette: colors used for painted subtrees (stacked bars)
  • width, height: widget size in pixels
  • sample_font_size, sample_label_margin, sample_label_space
  • sample_magnify, sample_show_all
  • rel_width, rel_height, rel_space
  • legend_mode, legend_x_start, legend_spacing
  • hclust_order: optional hierarchical reordering of rows/columns

Internally, phylobar() ensures that the tree has node labels and that the abundance matrix has row/column names. If they’re missing, helper check_inputs() creates sensible defaults (e.g., sample_1, sample_2).

Color Palette

If a palette is not provided, phylobar uses a default set of six colors. It is possible to supply own vector of hex colors or R color names.

# Custom qualitative palette (as many colors as you want; repeats if needed)
my_palette <- c(
    "#4E79A7", "#F28E2B", "#E15759",
    "#76B7B2", "#59A14F", "#EDC948"
)
phylobar(samples, tree, palette = my_palette)

Widget Size

By default the widget adapts to the container. Fix its size by:

phylobar(samples, tree,
    width = 800,
    height = 500
)

Sample Label Styling

Control sample label font size, spacing, and hover magnification.

phylobar(samples, tree,
    width = 800, height = 500,
    sample_font_size = 10,
    sample_label_margin = 10, # space between labels and bars
    sample_label_space = 100, # reserved margin for labels
    sample_magnify = 1.3, # how much to enlarge labels on hover
    sample_show_all = TRUE
)

Tree-bar Layout Ratio

Change how much horizontal and vertical space the tree occupies:

  • rel_width: fraction of total width reserved for the tree panel (default 0.4)
  • rel_height: fraction of total height for the tree panel (default 0.85)
  • rel_space: pixels between the tree and bar panels (default 10)
phylobar(
    samples, tree,
    width = 800, height = 500,
    sample_label_space = 100,
    sample_magnify = 1.3,
    rel_width = 0.2, # narrower tree
    rel_height = 0.70, # shorter tree (more space for legend)
    rel_space = 14 # larger gap between panels
)

Legend Placement

Choose whether painted subtree labels appear in a separate legend (legend_mode = TRUE, default) or placed inside the tree (legend_mode = FALSE). legend_x_start and legend_spacing can also be adjusted to control the legen position.

# Legend below the tree (default)
phylobar(
    samples, tree,
    width = 800, height = 500,
    sample_label_space = 100,
    sample_magnify = 1.3,
    legend_mode = TRUE,
    legend_x_start = 20, # horizontal start in pixels
    legend_spacing = 20 # vertical spacing between legend items in pixels
)
# Put labels inside the tree instead of a separate legend
phylobar(
    samples, tree,
    width = 800, height = 500,
    sample_label_space = 100,
    sample_magnify = 1.3,
    legend_mode = FALSE,
    legend_x_start = 20, # horizontal start in pixels
    legend_spacing = 20 # vertical spacing between legend items in pixels
)

Optional Hierarchical Reordering

hclust_order = TRUE (default) reorders samples/features by hierarchical clustering, which can make patterns more visible. Turn it off to preserve original order:

# Keep the input order as-is
phylobar(
    samples, tree,
    width = 800, height = 500,
    sample_label_space = 100,
    sample_magnify = 1.3,
    hclust_order = FALSE
)

Session Info 

sessionInfo()
#> R version 4.5.1 (2025-06-13)
#> Platform: aarch64-apple-darwin20
#> Running under: macOS Tahoe 26.3
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
#> 
#> locale:
#> [1] C.UTF-8/C.UTF-8/C.UTF-8/C/C.UTF-8/C.UTF-8
#> 
#> time zone: America/Chicago
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] phylobar_0.99.0  ape_5.8-1        BiocStyle_2.36.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] Matrix_1.7-4        jsonlite_2.0.0      compiler_4.5.1     
#>  [4] BiocManager_1.30.27 Rcpp_1.1.1          parallel_4.5.1     
#>  [7] cluster_2.1.8.2     jquerylib_0.1.4     systemfonts_1.3.1  
#> [10] textshaping_1.0.4   yaml_2.3.12         fastmap_1.2.0      
#> [13] lattice_0.22-9      R6_2.6.1            generics_0.1.4     
#> [16] igraph_2.2.1        knitr_1.51          htmlwidgets_1.6.4  
#> [19] bookdown_0.46       desc_1.4.3          bslib_0.10.0       
#> [22] rlang_1.1.7         fastmatch_1.1-8     cachem_1.1.0       
#> [25] xfun_0.56           quadprog_1.5-8      fs_1.6.6           
#> [28] sass_0.4.10         otel_0.2.0          cli_3.6.5          
#> [31] pkgdown_2.2.0       magrittr_2.0.4      phangorn_2.12.1    
#> [34] digest_0.6.39       grid_4.5.1          lifecycle_1.0.5    
#> [37] nlme_3.1-168        vctrs_0.7.1         evaluate_1.0.5     
#> [40] codetools_0.2-20    ragg_1.5.0          purrr_1.2.1        
#> [43] rmarkdown_2.30      tools_4.5.1         pkgconfig_2.0.3    
#> [46] htmltools_0.5.9