## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    message = FALSE
)

## ----example_data-------------------------------------------------------------
library(ape)
library(phylobar)

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

phylobar(samples, tree)

## ----palette_example----------------------------------------------------------
# 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--------------------------------------------------------------
phylobar(samples, tree,
    width = 800,
    height = 500
)

## ----sample_label_styling-----------------------------------------------------
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
)

## ----layout_ratio-------------------------------------------------------------
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_below-------------------------------------------------------------
# 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
)

## ----legend_inside------------------------------------------------------------
# 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_no----------------------------------------------------------------
# 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------------------------------------------------------------------
sessionInfo()