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 pixelssample_font_size, sample_label_margin, sample_label_spacesample_magnify, sample_show_allrel_width, rel_height, rel_spacelegend_mode, legend_x_start, legend_spacinghclust_order: optional hierarchical reordering of rows/columnsInternally, 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).
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)By default the widget adapts to the container. Fix its size by:
phylobar(samples, tree,
width = 800,
height = 500
)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
)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
)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
)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
)sessionInfo()
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