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 STRU...
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| Published in | SpringerPlus Vol. 3; no. 1; pp. 431 - 3 |
|---|---|
| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
Cham
Springer International Publishing
13.08.2014
Springer Nature B.V |
| Subjects | |
| Online Access | Get full text |
| ISSN | 2193-1801 2193-1801 |
| DOI | 10.1186/2193-1801-3-431 |
Cover
| Abstract | 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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| AbstractList | 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. 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. 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.BACKGROUNDUnderstanding 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.RESULTSWe 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.CONCLUSIONThe 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. 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. |
| ArticleNumber | 431 |
| Author | Naik, V Girish Bindroo, Bharat Bushan Ramasamy, Ramesh Krishnan Ramasamy, Sumathy |
| Author_xml | – sequence: 1 givenname: Ramesh Krishnan surname: Ramasamy fullname: Ramasamy, Ramesh Krishnan organization: Molecular Biology Laboratory-1, Host Plant Improvement, Central Sericultural Research and Training Institute – sequence: 2 givenname: Sumathy surname: Ramasamy fullname: Ramasamy, Sumathy organization: Bioinformatics Centre, Central Sericultural Research and Training Institute – sequence: 3 givenname: Bharat Bushan surname: Bindroo fullname: Bindroo, Bharat Bushan organization: Molecular Biology Laboratory-1, Host Plant Improvement, Central Sericultural Research and Training Institute, Bioinformatics Centre, Central Sericultural Research and Training Institute – sequence: 4 givenname: V Girish surname: Naik fullname: Naik, V Girish email: vgirishnaik@yahoo.com organization: Molecular Biology Laboratory-1, Host Plant Improvement, Central Sericultural Research and Training Institute |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/25152854$$D View this record in MEDLINE/PubMed |
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| ContentType | Journal Article |
| Copyright | 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 ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. SpringerPlus is a copyright of Springer, 2014. Ramasamy et al.; licensee Springer. 2014 |
| Copyright_xml | – notice: 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 ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. – notice: SpringerPlus is a copyright of Springer, 2014. – notice: Ramasamy et al.; licensee Springer. 2014 |
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| DOI | 10.1186/2193-1801-3-431 |
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| Keywords | CLUMPP DISTRUCT Shiny STRUCTURE HARVESTER R program |
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| References | Jakobsson, Rosenberg (CR3) 2007; 23 Evanno, Regnaut, Goudet (CR2) 2005; 14 Krishnan, Sumathy, Ramesh, Bindroo, Naik (CR4) 2014 CR5 Pritchard, Stephens, Donnelly (CR6) 2000; 155 Rosenberg (CR7) 2004; 4 Wickham (CR8) 2009 Earl (CR1) 2012; 4 1135_CR5 M Jakobsson (1135_CR3) 2007; 23 DA Earl (1135_CR1) 2012; 4 RR Krishnan (1135_CR4) 2014 JK Pritchard (1135_CR6) 2000; 155 NA Rosenberg (1135_CR7) 2004; 4 G Evanno (1135_CR2) 2005; 14 H Wickham (1135_CR8) 2009 17485429 - Bioinformatics. 2007 Jul 15;23(14):1801-6 15969739 - Mol Ecol. 2005 Jul;14(8):2611-20 10835412 - Genetics. 2000 Jun;155(2):945-59 |
| References_xml | – volume: 4 start-page: 137 issue: 1 year: 2004 end-page: 138 ident: CR7 article-title: DISTRUCT: a program for the graphical display of population structure publication-title: Mol Ecol Notes doi: 10.1046/j.1471-8286.2003.00566.x – volume: 23 start-page: 1801 issue: 14 year: 2007 end-page: 1806 ident: CR3 article-title: CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure publication-title: Bioinformatics doi: 10.1093/bioinformatics/btm233 – year: 2014 ident: CR4 article-title: SimEli: Similarity Elimination method for sampling distant entries in development of core collections publication-title: Crop Sci – ident: CR5 – volume: 155 start-page: 945 year: 2000 end-page: 959 ident: CR6 article-title: Inference of population structure using multilocus genotype data publication-title: Genetics – volume: 14 start-page: 2611 issue: 8 year: 2005 end-page: 2620 ident: CR2 article-title: Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study publication-title: Mol Ecol doi: 10.1111/j.1365-294X.2005.02553.x – year: 2009 ident: CR8 publication-title: ggplot2: elegant graphics for data analysis doi: 10.1007/978-0-387-98141-3 – volume: 4 start-page: 359 issue: 2 year: 2012 end-page: 361 ident: CR1 article-title: STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method publication-title: Conserv Genet Resour doi: 10.1007/s12686-011-9548-7 – volume: 23 start-page: 1801 issue: 14 year: 2007 ident: 1135_CR3 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btm233 – volume-title: ggplot2: elegant graphics for data analysis year: 2009 ident: 1135_CR8 doi: 10.1007/978-0-387-98141-3 – ident: 1135_CR5 – volume: 155 start-page: 945 year: 2000 ident: 1135_CR6 publication-title: Genetics doi: 10.1093/genetics/155.2.945 – volume: 4 start-page: 359 issue: 2 year: 2012 ident: 1135_CR1 publication-title: Conserv Genet Resour doi: 10.1007/s12686-011-9548-7 – volume: 4 start-page: 137 issue: 1 year: 2004 ident: 1135_CR7 publication-title: Mol Ecol Notes doi: 10.1046/j.1471-8286.2003.00566.x – volume-title: Crop Sci year: 2014 ident: 1135_CR4 – volume: 14 start-page: 2611 issue: 8 year: 2005 ident: 1135_CR2 publication-title: Mol Ecol doi: 10.1111/j.1365-294X.2005.02553.x – reference: 10835412 - Genetics. 2000 Jun;155(2):945-59 – reference: 15969739 - Mol Ecol. 2005 Jul;14(8):2611-20 – reference: 17485429 - Bioinformatics. 2007 Jul 15;23(14):1801-6 |
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Understanding structure of the population is one of the major objective of many genetic studies. The program STRUCTURE is commonly used to infer... Understanding structure of the population is one of the major objective of many genetic studies. The program STRUCTURE is commonly used to infer population... Background Understanding structure of the population is one of the major objective of many genetic studies. The program STRUCTURE is commonly used to infer... Background: Understanding structure of the population is one of the major objective of many genetic studies. The program STRUCTURE is commonly used to infer... |
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| Title | STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface |
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