README.md

In ggtaxplot: Create Plots to Visualize Taxonomy

ggtaxplot

Introduction

ggtaxplot is an R package designed to process and visualize taxonomic data through a taxonomic river plot. This package is ideal for researchers and data scientists who need to visualize taxonomic data.

Description

The ggtaxplot function processes data and generates a taxonomic river plot, allowing users to visualize the distribution of taxa across different samples.

Installation

You can install the ggtaxplot package from GitLab using the following command:

devtools::install_git("https://gitlab.com/ccoclet/ggtaxplot.git")

Usage

To use the ggtaxplot function, you can follow the example below:

library(ggtaxplot)

# Example data frame
data <- data.frame(
  ID = c("ID1", "ID2", "ID3"),
  Taxonomy = c("d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia",
               "d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus",
               "d__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Corynebacteriales;f__Corynebacteriaceae;g__Corynebacterium")
)

# Generate the river plot
plot <- ggtaxplot(data)
print(plot)

Arguments

• data: A data frame containing two columns: ID and Taxonomy.
• ID_col: A column with ID values (default is "ID").
• tax_col: A column with Taxonomy (default is "Taxonomy").
• threshold: A numeric threshold for filtering low-abundance taxa (default is 2).
• custom_colors: Optional custom colors assigned to phyla.

Value

The function returns a ggplot2 object of the river plot, which can be further customized using ggplot2 functions.

Support

For any issues or questions, please open an issue on the GitLab repository or contact the maintainer.

Contributing

Contributions are welcome! Please fork the repository and submit a pull request with your changes.

Authors and Acknowledgment

Thank you to all contributors who have helped improve ggtaxplot.

License

This project is licensed under the GPL-3 License.

Project Status

Development is ongoing. Contributions and feedback are encouraged to enhance the functionality of ggtaxplot.

ggtaxplot documentation built on April 4, 2025, 4:39 a.m.