---
title: "Publication-Ready Output"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Publication-Ready Output}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 10,
  fig.height = 7
)
```

## Color-Blind Friendly Palettes

Rclade defaults to the `viridis` palette, which is:
- Color-blind friendly
- Grayscale friendly
- Perceptually uniform

```{r palette}
library(Rclade)
data(example_tree)

# Default viridis palette
p <- plot_timetree(example_tree, rank = "phylum",
                   taxonomy_format = "GTDB",
                   add_timescale = FALSE)
print(p)
```

## Custom Color Mapping

```{r custom_colors}
# 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"))
print(p)
```

## Legend Placement

```{r legend}
# Inside the plot (default)
p <- plot_timetree(example_tree, rank = "phylum",
                   taxonomy_format = "GTDB",
                   add_timescale = FALSE,
                   legend_position = c(0.05, 0.85))

# Standard positions
p <- plot_timetree(example_tree, rank = "phylum",
                   taxonomy_format = "GTDB",
                   add_timescale = FALSE,
                   legend_position = "right")
```

## Clade Labels

```{r clade_labels}
p <- plot_timetree(example_tree, rank = "phylum",
                   taxonomy_format = "GTDB",
                   add_timescale = FALSE,
                   show_clade_label = TRUE)
print(p)
```

## Taxonomy Quality Report

Before finalizing your figure, verify label parsing quality:

```{r quality}
summarize_taxonomy_quality(example_tree$tip.label, format = "GTDB")
```

## Batch Processing

Process multiple tree files at once:

```{r batch, eval = FALSE}
batch_plot(input_dir = "trees/",
           output_dir = "figures/",
           pattern = "*.tre",
           rank = "phylum",
           taxonomy_format = "GTDB")
```

## Reproducibility

```{r reproducibility, eval = FALSE}
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:

- Yu G, Smith DK, Zhu H, Guan Y, Lam TT-Y (2017). "ggtree: an R package for
  visualization and annotation of phylogenetic trees with their covariates and
  other associated data." *Methods in Ecology and Evolution*, 8(1), 28-36.
  doi:10.1111/2041-210X.12628
- Gearty W (2025). "deeptime: an R package that facilitates highly
  customizable and reproducible visualizations of data over geological time
  intervals." *Big Earth Data*. doi:10.1080/20964471.2025.2537516

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