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STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface

BACKGROUND: 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 STR...

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Autores principales: Ramasamy, Ramesh Krishnan, Ramasamy, Sumathy, Bindroo, Bharat Bushan, Naik, V Girish
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4141070/
https://www.ncbi.nlm.nih.gov/pubmed/25152854
http://dx.doi.org/10.1186/2193-1801-3-431
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author Ramasamy, Ramesh Krishnan
Ramasamy, Sumathy
Bindroo, Bharat Bushan
Naik, V Girish
author_facet Ramasamy, Ramesh Krishnan
Ramasamy, Sumathy
Bindroo, Bharat Bushan
Naik, V Girish
author_sort Ramasamy, Ramesh Krishnan
collection PubMed
description BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.
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spelling pubmed-41410702014-08-22 STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface Ramasamy, Ramesh Krishnan Ramasamy, Sumathy Bindroo, Bharat Bushan Naik, V Girish Springerplus Software BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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. Springer International Publishing 2014-08-13 /pmc/articles/PMC4141070/ /pubmed/25152854 http://dx.doi.org/10.1186/2193-1801-3-431 Text en © Ramasamy et al.; licensee Springer. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
spellingShingle Software
Ramasamy, Ramesh Krishnan
Ramasamy, Sumathy
Bindroo, Bharat Bushan
Naik, V Girish
STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface
title STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface
title_full STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface
title_fullStr STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface
title_full_unstemmed STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface
title_short STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface
title_sort structure plot: a program for drawing elegant structure bar plots in user friendly interface
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4141070/
https://www.ncbi.nlm.nih.gov/pubmed/25152854
http://dx.doi.org/10.1186/2193-1801-3-431
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