The Ultimate Guide to the ggpicrust2 Package in R

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Explore valuable documentation and insights to make the most of the ggpicrust2 package in R. Get ready to unlock the full potential of the ggpicrust2 package!

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What is the ggpicrust2 package?

In this section, we’ll delve into the fundamental aspects and key features of the package.

ggpicrust2 is a package designed for creating plots from the outputs of PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), a bioinformatics software package for predicting functional profiles of microbial communities from 16S rRNA marker gene surveys.

Title: Make 'PICRUSt2' Output Analysis and Visualization Easier
Description: Provides a convenient way to analyze and visualize 'PICRUSt2' output with pre-defined plots and functions. Allows for generating statistical plots about microbiome functional predictions and offers customization options. Features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. Streamlines the 'PICRUSt2' analysis and visualization process. For more details, see Yang et al. (2023) .
Author: Chen Yang [aut, cre], Liangliang Zhang [aut]
Maintainer: Chen Yang

How to install the ggpicrust2 package?

In this section, we’ll walk you through the process of installing and loading the ggpicrust2 package. By following these steps, you can seamlessly add new functions, datasets, and other resources to your R environment for a more robust workflow.

# Install the {Package} package if it's not already installed
if (!require("{Package}")) {
    install.packages("{Package}")
}


# Load the {Package} package
library("{Package}")

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What package information should you know?

In this section, we’ll go over the technical aspects of the ggpicrust2 package.

Key features

Datasets: Many R packages include built-in datasets that you can use to familiarize yourself with their functionalities. To identify built-in datasets. To identify the datasets for the ggpicrust2 package, visit our database of R datasets.
Vignettes: R vignettes are documents that include examples for using a package. To view the list of available vignettes for the ggpicrust2 package, you can visit our visit our database of R vignettes.
Citation: Citing R packages in your publications is important as it recognizes the contributions of the developers. To find citation information for the ggpicrust2 package, visit our database of R package citations.

Technical details

License type: MIT + file LICENSE. For license details, visit the Open Source Initiative website.
Compilation requirements: Some R packages include internal code that must be compiled for them to function correctly. The ggpicrust2 package does not have compilation requirements.
Required dependencies: A required dependency refers to another package that is essential for the functioning of the main package. The ggpicrust2 package has the following required dependencies: R (>= 3.5.0).
Suggested dependencies: A suggested dependency adds extra features to the main package, but the main package can work without it. The ggpicrust2 package has the following suggested dependencies: Biobase, KEGGREST, ComplexHeatmap, ggplotify, BiocGenerics, magrittr, utils, knitr, rmarkdown.
External dependencies: External dependencies are other packages that the main package depends on for linking at compile time. The ggpicrust2 package does not use any external sources.
Imported packages: Importing packages allows developers to leverage existing code and functionalities without having to reinvent the wheel. The ggpicrust2 package has the following imported packages: ALDEx2, aplot, DESeq2, dplyr, edgeR, GGally, ggplot2, grid, ggh4x, lefser, limma, Maaslin2, metagenomeSeq, MicrobiomeStat, readr, SummarizedExperiment, tibble, tidyr, ggprism, patchwork, circlize.
Enhancements: Enhancements help developers expand the capabilities of their packages without starting from scratch. The ggpicrust2 package has no enhancements.

How to get help with the ggpicrust2 package?

In this section, we’ll discuss a variety of available resources for getting help with the ggpicrust2 package.

Key resources

The help() function: R’s built-in help system is a handy tool to find documentation. You can use the help("ggpicrust2") function to retrieve detailed information, examples, and usage instructions. Alternatively, you can use the ? operator as a shortcut.
Package website: The ggpicrust2 package has a dedicated website. You can visit: https://github.com/cafferychen777/ggpicrust2.
Developer support: You can email Chen Yang . For contact information, visit our R community directory.

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