R语言在生物科学研究绘图中的应用
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摘要
R语言具有强大的数据分析处理和可视化绘图功能,可以在Window、Linux以及Mac系统上使用,并且根据其编写新代码或调整已有代码可轻松实现科研中数据呈现与图形绘制的要求.然而其代码学习较为艰难、R-package使用复杂,所以未受到科研新手的青睐.基于生物科学相关领域的背景,整理汇集已出版的文献、公共数据库以及国家统计局中提供的数据,使用R语言、R编辑器RStudio并载入相关的R-package绘制出地图、热图、关联网络图、韦恩图和柱形图等高质量的图片,并提供相应的脚本与说明,以方便生物科研人员直接更改使用.本研究对生物科研中合理、直观地表述研究结果提供了良好的范例,并进行了详细讨论,且与其他绘图软件作了比较,以期R语言能够成为生物科学领域科研工作者入门学习、研究应用中绘制图片的首选工具.
The R programming language offers powerful statistical analysis, data processing, and visualization capabilities, which can run on Windows, Linux, and Mac operating systems; the software allows users to show scientific research data through graphics by writing new code or adjusting existing code. However, it is difficult to learn R'sprogramming code and use R packages, so R is not commonly favored by novices in the scientific research community. Based on the context of bioscience fields and data from published papers, public databases, and the National Bureau of Statistics, this study demonstrates how to plot high quality maps,heat maps, functional networks, Venn diagrams, and column charts using R, R Studio, and R-packages. To facilitate the use of R, we offer detailed scripts for biological researchers. After comparing R with other graphing software, this study provides good examples and discussions of how to reasonably and intuitively present results in biological research. We hope R will become the preferred plotting tool for elementary biological researchers in their learning and research activities.
The R programming language offers powerful statistical analysis, data processing, and visualization capabilities, which can run on Windows, Linux, and Mac operating systems; the software allows users to show scientific research data through graphics by writing new code or adjusting existing code. However, it is difficult to learn R'sprogramming code and use R packages, so R is not commonly favored by novices in the scientific research community. Based on the context of bioscience fields and data from published papers, public databases, and the National Bureau of Statistics, this study demonstrates how to plot high quality maps,heat maps, functional networks, Venn diagrams, and column charts using R, R Studio, and R-packages. To facilitate the use of R, we offer detailed scripts for biological researchers. After comparing R with other graphing software, this study provides good examples and discussions of how to reasonably and intuitively present results in biological research. We hope R will become the preferred plotting tool for elementary biological researchers in their learning and research activities.
引文
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[20]王怀亮.基于R语言的统计数据柱形图的实现[J].电子技术,2013(8):78-80.
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[29] ITO K, MURPHY D. Application of ggplot2 to pharmacometric graphics[J]. Cpt Pharmacometrics&Systems Pharmacology, 2013, 2(10):1-16.
[30] SARKAR, DEEPAYAN. Lattice:Multivariate Data Visualization with R[M]. New York:Springer, 2008.
[31] CHEN H, BOUTROS P C. VennDiagram:A package for the generation of highly-customizable Venn and Euler diagrams in R[J]. Bmc Bioinformatics, 2011, 12(1):35-41.
[32] FOSTER Z S, SHARPTON T J, GRUNWALD N J. Metacoder:An R package for visualization and manipulation of community taxonomic diversity data[J]. Plos Computational Biology, 2017, 13(2):e1005404.
[33] BENNETT D J, SUTTON M D,TURVEY S T. Treeman:An R package for efficient and intuitive manipulation of phylogenetic trees[J]. Bmc Research Notes, 2017, 10(1):30-39.
[34] MCKENZIE A T, KATSYV I, SONG W M, et al. DGCA:A comprehensive R package for differential gene correlation analysis[J]. Bmc Systems Biology, 2016, 10(1):106-130.
[35] KNAUS B J, GRUNWALD N J. Vcfr:A package to manipulate and visualize variant call format data in r[J].Molecular Ecology Resources, 2017, 17(1):44-53.
[36] TITECA K, MEYSMAN P, LAUKENS K, et al. Sfinx:An R package for the elimination of false positives from affinity purification-mass spectrometry datasets.[J].Bioinformatics, 2017, 33(12):1902-1904.
[37] MEI H, LI L, JIANG F, et al. snpGeneSets:An R package for genome-wide study annotation[J]. G3(Bethesda,Md.), 2016, 6(12):4087-4095.
[38] NOTA B. Gogadget:An R package for interpretation and visualization of GO enrichment results[J]. Molecular Informatics, 2017, 36:5-6.
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[40]房世波,齐月,韩国军,等.1961-2010年中国主要麦区冬春气象干早趋势及其可能影响[J].中国农业科学,2014, 47(9):1754-1763.
[41]国家统计局.国家数据[EB/OL].[2017-05-15]. http://data.stats.gov.cn/easyquery.htm?cn=E0103.
[42]丁香园.热图的解读与应用[EB/OL].(2016-02-01)[2017-05-15].http://www.dxy.cn/bbs/topic/32836042-source=rss.
[43] CARUSO S,MIRAGLIA R, MARUZZELLI L, et al. Chaperone activity of tobacco HSP18, a small heat-shock protein, is inhibited by ATP[J]. Plant Journal, 2000, 23(6):703-713.
[44]张厚品.韦思图的起源[J].数学教学,2005(7):48-49.
[45] MICALLEF L, RODGERS P. Euler APE:Drawing area-proportional 3-venn diagrams using ellipses[J]. Plos One, 2014, 9(7):e101717.
[46] KOSTAL V, KORBELOVA J, STETINA T, et al. Physiological basis for low-temperature survival and storage of quiescent larvae of the fruit fly Drosophila melanogaster[J]. Scientific Reports, 2016(6):32346-32356.
[47]李红,张元湖.应用DPPH?法测定苹果提取物的抗氧化能力[J].山东农业大学学报(自然科学版),2005, 36(1):35-38.
[48]孙存普.自由基生物学导论[M].合肥:中国科学技术大学出版社,1999.
[49] JIN SK, HA S R, CHOI J S.Effect of Caesalpinia sappan L. extract on physico-chemical properties of emulsiontype pork sausage during cold storage[J]. Meat Science, 2015, 110:245-252.
[50] MENTE S, KUHN M. The use of the R language for medicinal chemistry applications[J]. Current Topics in Medicinal Chemistry, 2012, 12(18):1957-1964.
[2] CARSON M A, BASILIKO N. Approaches to R education in Canadian universities[J]. F1000research, 2016(5):1-18.
[3] SEIFERT E. OriginPro 9.1:Scientific data analysis and graphing software-Software review[J]. Journal of Chemical Information&Modeling, 2014, 54(5):1552.
[4] WASS J A. SigmaPlot 11:Now with total sigmaStat integration[J]. Scientific Computing, 2009, 26(1):21-25.
[5] MCCORMICK K, SALCEDO J. SPSS statistics for data analysis and visualization[J]. Drug Testing&Analysis,2017, 1(6):250-266.
[6] GENTLEMAN R, HUBER W, CAREY V J. R Language[M]. New York:Springer Berlin Heidelberg, 2011.
[7] GANCHEV D H. Using R language for statistical computing for pesticide application calculations[J]. MAYFEB Journal of Agricultural Science, 2016(1):10-26.
[8] FELD C K, SEGURADO P, GUTIERREZ-CANOVAS C. Analysing the impact of multiple stressors in aquatic biomonitoring data:A'cookbook'with applications in R[J]. Science of the Total Environment, 2016, 573:1320-1339.
[9] GUENZI D, FRATIANNI S, BORASO R, et al. CondMerg:An open source implementation in R language of conditional merging for weather radars and rain gauges observations[J]. Earth Science Informatics, 2016, 10(1):1-9.
[10] LI J, WANG J, CHEN Y, et al. A prognostic 4-gene expression signature for squamous cell lung carcinoma[J].Journal of Cellular Physiology, 2017, 232(12):3702-3713.
[11] ZHAI J, HSU C H, DAYE Z J. Ridle for sparse regression with mandatory covariates with application to the genetic assessment of histologic grades of breast cancer[J]. Bmc Medical Research Methodology, 2017, 17(1):12-24.
[12] WANG Z, ZHANG C, LIU X, et al. Molecular and clinical characterization of PD-L1 expression at transcriptional level via 976 samples of brain glioma. Oncoimmunology[J], 2016, 5(11):e1196310.
[13] OH D H, KIM I B, KIM S H, et al. Predicting autism spectrum disorder using blood-based gene expression signatures and machine learning[J]. Clin Psychopharmacol Neurosci, 2017, 15(1):47-52.
[14] WOJCIECHOWSKI J, HOPKINS A M, UPTON R N. Interactive pharmacometric applications using R and the shiny package[J]. CPT Pharmacometrics Syst Pharmacol, 2015, 4(3):e00021.
[15] LARRIBA Y, RUEDA C, FERNANDEZ M A, et al. Order restricted inference for oscillatory systems for detecting rhythmic signals.[J]. Nucleic Acids Research, 2016, 44(22):e163.
[16] PARADIS E, GOSSELIN T, GRUNWALD N J, et al. Towards an integrated ecosystem of R packages for the analysis of population genetic data[J]. Molecular Ecology Resources, 2017, 17(1):1-4.
[17] MILLER F P, VANDOME A F, MCBREWSTER J, et al. R(programming language)[J]. Betascript Publishing,2010, 6(2):36-40.
[18] CHAPMAN C, FEIT E M D. An Overview of the R Language[M]//CHAPMAN C, FEIT E M D. R for Marketing Research and Analytics. New York:Springer International Publishing, 2015.
[19]王怀亮.箱须图在识别统计数据异常值中的作用及R语言实现[J].商业经济,2011(5):64-65.
[20]王怀亮.基于R语言的统计数据柱形图的实现[J].电子技术,2013(8):78-80.
[21]石蕾.R语言在藓类形态与遗传变异研究中的应用[D].上海:上海师范大学,2015.
[22]兰国玉,陈伟,王继坤,等.R语言在橡胶林动态监测地形图绘制方面的应用[J].热带农业科学,2013, 33(3):50-53.
[23]纪相禹.基于R语言的差异表达基因检测研究[D].长春:吉林大学.2011
[24] DOBRE G R. R Language:Statistical computing and graphics for modeling hydrologic time series[J]. Mathematical Modeling in Civil Engineering, 2014, 10(4):9-18.
[25] CRAN. The Comprehensive R Archive Network[DB/OL].[2017-05-01]. https://cran.r-project.org/.
[26] HORNIK K. The comprehensive R archive network[J]. Wiley Interdisciplinary Reviews Computational Statistics,2012, 4(4):394-398.
[27] IHAKA R, GENTLEMAN R. R:A language for data analysis and graphics[J]. Journal of Computational&Graphical Statistics, 1996, 5(3):299-314.
[28] VANCE A. Data analysts captivated by R's power[N]. New York Times, 2009-01-06(Business Computing).
[29] ITO K, MURPHY D. Application of ggplot2 to pharmacometric graphics[J]. Cpt Pharmacometrics&Systems Pharmacology, 2013, 2(10):1-16.
[30] SARKAR, DEEPAYAN. Lattice:Multivariate Data Visualization with R[M]. New York:Springer, 2008.
[31] CHEN H, BOUTROS P C. VennDiagram:A package for the generation of highly-customizable Venn and Euler diagrams in R[J]. Bmc Bioinformatics, 2011, 12(1):35-41.
[32] FOSTER Z S, SHARPTON T J, GRUNWALD N J. Metacoder:An R package for visualization and manipulation of community taxonomic diversity data[J]. Plos Computational Biology, 2017, 13(2):e1005404.
[33] BENNETT D J, SUTTON M D,TURVEY S T. Treeman:An R package for efficient and intuitive manipulation of phylogenetic trees[J]. Bmc Research Notes, 2017, 10(1):30-39.
[34] MCKENZIE A T, KATSYV I, SONG W M, et al. DGCA:A comprehensive R package for differential gene correlation analysis[J]. Bmc Systems Biology, 2016, 10(1):106-130.
[35] KNAUS B J, GRUNWALD N J. Vcfr:A package to manipulate and visualize variant call format data in r[J].Molecular Ecology Resources, 2017, 17(1):44-53.
[36] TITECA K, MEYSMAN P, LAUKENS K, et al. Sfinx:An R package for the elimination of false positives from affinity purification-mass spectrometry datasets.[J].Bioinformatics, 2017, 33(12):1902-1904.
[37] MEI H, LI L, JIANG F, et al. snpGeneSets:An R package for genome-wide study annotation[J]. G3(Bethesda,Md.), 2016, 6(12):4087-4095.
[38] NOTA B. Gogadget:An R package for interpretation and visualization of GO enrichment results[J]. Molecular Informatics, 2017, 36:5-6.
[39]中国测绘网.地图制图概念(词汇解释)[EB/OL].(2013-08-28)[2017-05-15]. http://www.cehui8.com/zhuanti/map/20130828/1191.html.
[40]房世波,齐月,韩国军,等.1961-2010年中国主要麦区冬春气象干早趋势及其可能影响[J].中国农业科学,2014, 47(9):1754-1763.
[41]国家统计局.国家数据[EB/OL].[2017-05-15]. http://data.stats.gov.cn/easyquery.htm?cn=E0103.
[42]丁香园.热图的解读与应用[EB/OL].(2016-02-01)[2017-05-15].http://www.dxy.cn/bbs/topic/32836042-source=rss.
[43] CARUSO S,MIRAGLIA R, MARUZZELLI L, et al. Chaperone activity of tobacco HSP18, a small heat-shock protein, is inhibited by ATP[J]. Plant Journal, 2000, 23(6):703-713.
[44]张厚品.韦思图的起源[J].数学教学,2005(7):48-49.
[45] MICALLEF L, RODGERS P. Euler APE:Drawing area-proportional 3-venn diagrams using ellipses[J]. Plos One, 2014, 9(7):e101717.
[46] KOSTAL V, KORBELOVA J, STETINA T, et al. Physiological basis for low-temperature survival and storage of quiescent larvae of the fruit fly Drosophila melanogaster[J]. Scientific Reports, 2016(6):32346-32356.
[47]李红,张元湖.应用DPPH?法测定苹果提取物的抗氧化能力[J].山东农业大学学报(自然科学版),2005, 36(1):35-38.
[48]孙存普.自由基生物学导论[M].合肥:中国科学技术大学出版社,1999.
[49] JIN SK, HA S R, CHOI J S.Effect of Caesalpinia sappan L. extract on physico-chemical properties of emulsiontype pork sausage during cold storage[J]. Meat Science, 2015, 110:245-252.
[50] MENTE S, KUHN M. The use of the R language for medicinal chemistry applications[J]. Current Topics in Medicinal Chemistry, 2012, 12(18):1957-1964.