Vignette rKOMICS application example

Abstract

The core features of the rKOMICS package include data aggregation, analyses and visualization that allows to examine, summarize and extract meaningful information from minicircle sequence alignments as obtained by KOMICS or a custom bioinformatic pipeline, and from USEARCH cluster format (UC) files as generated by USEARCH or VSEARCH. In addition to storing data files, rKOMICS stores the analyses and visualization results into single list objects that can be called by the user at a later stage. rKOMICS incorporates multiple methods of visualizations using the ggplot2 R package to plot the foundation of graphs. By adding ggplot2 functions to the rKOMICS visualization functions, the user has direct control over the finishing touches of the graph’s appearances. Our package also utilizes sample specific metadata that allows multi-group data visualizations to facilitate exploratory analysis. The overall data set can be examined using barplots, heatmaps, PCA plots and box plots that are generated for each specified minimum percent identity. This makes it possible to visualize population structure and diversity based on minicircle sequence composition. To show the functionality of rKOMICS, we performed an example analysis using whole-genome se quencing data from a recently published study on the history of diversification of the Leishmania brazilien sis species complex in Peru. This species complex comprises two closely related species: the lowland and zoonotic L. braziliensis parasite circulating in a diverse range of wild mammals in Neotropical rainforests, and the highland anthroponotic L. peruviana parasite that is largely endemic to the Pacific slopes of the Peruvian Andes. A total of 67 Leishmania parasites from 47 localities in Peru were cultured and subjected to whole genome sequencing.