flowDiv: a new pipeline for analyzing flow cytometric diversity
- Published
- Accepted
- Subject Areas
- Bioinformatics, Computational Biology, Ecology, Ecosystem Science, Data Science
- Keywords
- flow cytometry, cytometric diversity, R
- Copyright
- © 2018 Wanderley et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. flowDiv: a new pipeline for analyzing flow cytometric diversity. PeerJ Preprints 6:e26934v1 https://doi.org/10.7287/peerj.preprints.26934v1
Abstract
Flow cytometry (FCM) is a powerful analytical tool that is widely used worldwide, as it allows the depiction of the innate complexity of a vast range of biological systems in few seconds. It is a technique based on the spectroscopic properties of suspended particles that allows data to be graphically summarized by biplots, known as cytograms. Such versatility got raises to different analytical protocols which are commonly not interchangeable among expertise fields. In this sense, environmental sciences, in particular, faces major concerns when dealing with the adoption of non-specific protocols - a particularity essentially driven by the highly heterogeneous nature of environmental samples. Such intrinsic variety makes it difficult to adjust formal analytical protocols that both keep standardized mathematical rationales and retain a clear ecological meaning, namely when the focus of the analysis rely on the cytometric diversity - the quantitative evaluation of the differences among cytograms. Despite of the availability of promising tools conceived or adapted to approach cytometric diversity, most of them face common technical challenges, as perspective adjustment, dilution correction, resolution setup and enlightenment on the role of cytograms subregions to global diversity. To address such questions and harmonize formal mathematical rationales with coherent biological interpretation, we have developed flowDiv - a pipeline designed for environmental flow cytometry data analysis that handles data through consolidated macroecological methods to offer biologically apprehensive outputs. flowDiv was implemented using R language and has been published on CRAN (https://cran.r-project.org/web/packages/flowDiv/) with source code also available on GitHub (https://github.com/bmsw/flowDiv). Applied to a dataset from 31 freshwater bodies in Argentinian Patagonia, flowDiv uncovered significant aspects regrading environmental cytometric diversity, as its relation with taxonomic diversity and the role of environmental variables on cytometric diversity.
Author Comment
In this article we debate on the implementation of flowDiv, a pipeline for analyzing environmental flow cytometry data using multidimensional contingency tables, devised as an improvement and extension of Li's (1997) ideas. Here we also illustrate its rationale by successfully applying it to a dataset from 31 natural freshwater bodies in Argentinian Patagonia.