StackbarExtended: a user-friendly stacked bar-plot representation incorporating phylogenetic information and microbiota differential abundance analysis

Abstract

Background Microbial communities are mainly composed of bacteria, archaea, viruses and fungi, and are present in the gut, mouth, nose, skin, lungs, vagina, and bladder, among other places. In recent years, research has highlighted the critical role that these highly complex communities play in health and disease. Advances in sequencing technology have resulted in the development of high-dimensional data, which are challenging to effectively analyze and visualize. In this context, traditional stacked bar-plot visualizations, while widely used, fall short of conveying the fundamental phylogenic relationships between community members and are thus difficult to interpret. Methods StackbarExtended is implemented in native R, required version (≥ 4.0), and is platform independent, with its source code available on GitHub and archived on Zenodo. Results StackbarExtended allows for the plotting of relative abundance at user-defined taxonomic levels while displaying phylogenetic information using color gradients. Additionally, StackbarExtended integrates differential abundance statistics directly into the visualization process and performs clustering of low-abundance taxa. Conclusions StackbarExtended offers researchers a user-friendly tool for rapid visualization, presentation, and analysis of the microbiota composition.