STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface
- Ramesh Krishnan Ramasamy†1,
- Sumathy Ramasamy†2,
- Bharat Bushan Bindroo1, 2 and
- V Girish Naik1Email author
© Ramasamy et al.; licensee Springer. 2014
Received: 23 April 2014
Accepted: 6 August 2014
Published: 13 August 2014
Understanding structure of the population is one of the major objective of many genetic studies. The program STRUCTURE is commonly used to infer population structure using multi-locus genotype data. However, a tool with graphical-user interface is currently not available to visualize STRUCTURE bar plots.
We introduce STRUCTURE PLOT, a program for drawing STRUCTURE bar plots. The program generates publication ready, aesthetic STRUCTURE bar plots by using individual Q matrix from STRUCTURE or CLUMPP output. The program is very simple to use and includes variety of options like sorting bar by original order or by K, and selection of colors from R colors or RColorBrewer palette. Individual or population labels can be printed below or above the plot in any angle. Size of the graph and label can be defined, and option is provided to save plot in variety of picture formats in user defined resolution.
The program is implemented as a web application for online users and also as a standalone shiny application. Web application is compatible to majority of leading web browsers and standalone version can be launched using a simple R command. The program can be freely accessed at http://btismysore.in/strplot.
KeywordsDISTRUCT CLUMPP STRUCTURE HARVESTER R program Shiny
The program STRUCTURE (Pritchard et al. 2000) is one of the widely used genetic analysis software over the last decade to infer population structure and gene flow by using multi-locus genotypic data. STRUCTURE implements model based method to assign each individual to one assumed population (K) or more than one population, if it is an admixture. Estimating suitable assumed population size for the dataset is usually based on maximum likelihood (LnPD) value inferred from STRUCTURE run or delta K (Δk) value (Evanno et al. 2005). STRUCTURE HARVESTER (Earl 2012) program was designed to carry out downstream processing of STRUCTURE results to calculate Evanno’s Δk value and prepares input file for CLUMPP program (Jakobsson and Rosenberg 2007). CLUMPP program permutes replicated runs of STRUCTURE software to find a close match among iterated runs. CLUMPP results are used to generate bar graphs using DISTRUCT (Rosenberg 2004) program. DISTRUCT is a standalone program without Graphical User Interface (GUI), and the drawing parameters needs to be defined in a separate file. DISTRUCT returns the result file in postscript format and users have to install third-party software to convert postscript to the graphical format. To overcome these limitations, we introduce a user-friendly program – ‘STRUCTURE PLOT’ to draw elegant bar plots with graphical user interface.
Authors acknowledge all the three reviewers for their constructive and insightful comments, which improved the quality of the manuscript.
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