高三英语学术研究方法创新不断探索单选题30题及答案1.In academic research, where is the best place to start looking for relevant literature?A.The libraryB.The internetC.A professor's officeD.A friend's bookshelf答案：A。
在学术研究中，图书馆通常拥有丰富的学术资源，包括书籍、期刊等，是开始查找相关文献的最佳地方。
选项B 互联网上的信息可能不准确或不权威。
选项C 教授的办公室不是查找文献的主要场所。
选项D 朋友的书架上的书可能不具有学术性。
2.When searching for literature, which keyword should you avoid using?mon wordsB.Specific termsC.Technical jargonD.Academic phrases答案：A。
在查找文献时，应避免使用常见词汇，因为这样会得到大量不相关的结果。
选项B 特定术语、选项C 技术行话、选项D 学术短语都可以帮助缩小搜索范围。
3.Which of the following is NOT a reliable source of literature for academic research?A.Scholarly journalsB.Popular magazinesC.Academic booksD.Research papers答案：B。
学术研究中，可靠的文献来源包括学术期刊、学术书籍和研究论文。
流行杂志通常不具有学术性和权威性。
4.If you can't find a particular piece of literature in your local library, what should you do?A.Give upB.Ask a friendC.Try an online databaseD.Wait for it to appear答案：C。
Package‘gggenes’September5,2023Title Draw Gene Arrow Maps in'ggplot2'Version0.5.1Description A'ggplot2'extension for drawing gene arrow maps.Depends R(>=3.6)Imports grid(>=3.3.0),ggplot2(>=2.2.1),ggfittext(>=0.8.0),rlang(>=0.2.0)License GPL-2LazyData trueRoxygenNote7.2.3URL https:///gggenes/BugReports https:///wilkox/gggenes/issues/Suggests testthat,knitr,rmarkdown,vdiffr,spellingVignetteBuilder knitrEncoding UTF-8Language en-USNeedsCompilation noAuthor David Wilkins[aut,cre],Zachary Kurtz[ctb]Maintainer David Wilkins<****************>Repository CRANDate/Publication2023-09-0511:50:10UTCR topics documented:example_dummies (2)example_features (2)example_genes (3)geom_feature (4)geom_feature_label (5)12example_features geom_gene_arrow (7)geom_gene_label (8)geom_subgene_arrow (10)geom_subgene_label (11)make_alignment_dummies (13)theme_genes (14)Index15 example_dummies A set of example dummy alignment genes.DescriptionDummy genes,similar to those generated with make_alignment_dummies(),for example purposes only.Usageexample_dummiesFormatA data frame with eight rows and three variables:molecule the genomestart the start position of the dummyend the end position of the dummygene the name of the dummy geneexample_features A set of example genetic features.DescriptionGenetic features for example purposes only.Usageexample_featuresexample_genes3 FormatA data frame with23rows andfive variables:molecule the genomename the name of the featuretype the type of the featureposition the position of the featureforward is the feature oriented,and if so in the forward direction?example_genes A set of example genes.DescriptionGenes for example purposes only.Usageexample_genesexample_subgenesFormatA data frame with72rows and six variables:molecule the genomegene the name of the genestart the start position of the geneend the end position of the genestrand the strand of the geneorientation the orientation of the geneexample_subgenes(143rows)also contains:subgene the name of the subgenefrom the start position of the subgene segmentto the end position of the subgene segmentAn object of class data.frame with143rows and9columns.4geom_feature geom_feature A’ggplot2’geom to draw point genetic featuresDescriptiongeom_feature()draws lines to indicate the positions of point genetic features,for example restric-tion sites,origins of replication or transcription start sites.Usagegeom_feature(mapping=NULL,data=NULL,stat="identity",position="identity",na.rm=FALSE,show.legend=NA,inherit.aes=FALSE,feature_height=unit(3,"mm"),feature_width=unit(3,"mm"),arrowhead_width=unit(2,"mm"),...)Argumentsmapping,data,stat,position,na.rm,show.legend,inherit.aes,...As standard for ggplot2.inherit.aes is set to FALSE by default,as features arenot likely to share any plot aesthetics other than y.feature_height grid::unit()object giving the height of a feature above the molecule line.Can be set as a negative value to draw features below the line.Defaults to3mm.feature_width grid::unit()object giving the width of a feature(distance from the elbow to the tip of the arrow).Only relevant for oriented features.Defaults to3mm.arrowhead_widthgrid::unit()object giving the width of the arrowhead indicating the directionof an oriented feature.Only relevant for oriented features.Defaults to2mm.DetailsFeatures are drawn as vertical lines extending from the horizontal line representing the molecule.The position of the feature is expressed with the x aesthetic.Optionally,the forward aesthetic can be used to specific an orientation for the feature(e.g.the direction of transcription),in which case an angled arrowhead will be added.The forward aesthetic assumes that the x-axis is oriented in the normal direction,i.e.increasing from left to right;if it is not,the values in forward will need to be inverted manually.Aesthetics•x(required;position of the feature)•y(required;molecule)•forward(optional;if TRUE,or a value coercible to TRUE,the feature will be drawn with an arrowhead pointing right,if FALSE,pointing left,if NA,the feature will be drawn as a vertical line)•alpha•colour•linetype•sizeSee Alsogeom_feature_label()Examplesggplot2::ggplot(example_genes,ggplot2::aes(xmin=start,xmax=end,y=molecule,fill=gene))+ geom_gene_arrow()+geom_feature(data=example_features,ggplot2::aes(x=position,y=molecule,forward=forward))+ ggplot2::facet_wrap(~molecule,scales="free")geom_feature_label A’ggplot2’geom to add text labels to point genetic featuresDescriptiongeom_feature_label()adds text labels to features drawn with geom_feature().Usagegeom_feature_label(mapping=NULL,data=NULL,stat="identity",position="identity",na.rm=FALSE,show.legend=FALSE,inherit.aes=FALSE,feature_height=unit(4,"mm"),label_height=unit(3,"mm"),...)Argumentsmapping,data,stat,position,na.rm,show.legend,inherit.aes,...As standard for ggplot2.inherit.aes is set to FALSE by default,as features arenot likely to share any plot aesthetics other than y.feature_height grid::unit()object giving the height of the feature being labelled,and hence the distance of the label above or below the molecule line.Can be set as anegative value for features drawn below the line.Defaults to4mm,to alignlabels with the default height of geom_feature().label_height grid::unit()object giving the height of the label text.Defaults to3mm.DetailsStandard’ggplot2’aesthetics for text are supported(see Aesthetics).Aesthetics•x(required;position of the feature)•y(required;molecule)•label(required;the label text)•forward(optional;will draw text in the appropriate location for features with angled arrow-heads)•colour•size•alpha•family•fontface•angleSee Alsogeom_feature()Examplesggplot2::ggplot(example_genes,ggplot2::aes(xmin=start,xmax=end,y=molecule,fill=gene))+ geom_gene_arrow()+geom_feature(data=example_features,ggplot2::aes(x=position,y=molecule,forward=forward))+ geom_feature_label(data=example_features,ggplot2::aes(x=position,y=molecule,label=name,forward=forward))+ggplot2::facet_wrap(~molecule,scales="free")geom_gene_arrow7 geom_gene_arrow A’ggplot2’geom to draw genes as arrowsDescriptiongeom_gene_arrow()draws genes as arrows,allowing gene maps to be drawn.Usagegeom_gene_arrow(mapping=NULL,data=NULL,stat="identity",position="identity",na.rm=FALSE,show.legend=NA,inherit.aes=TRUE,arrowhead_width=grid::unit(4,"mm"),arrowhead_height=grid::unit(4,"mm"),arrow_body_height=grid::unit(3,"mm"),...)Argumentsmapping,data,stat,position,na.rm,show.legend,inherit.aes,...As standard for ggplot2.arrowhead_widthgrid::unit()object giving the width of the arrowhead.Defaults to4mm.Ifthe gene is drawn smaller than this width,only the arrowhead will be drawn,compressed to the length of the gene.arrowhead_heightgrid::unit()object giving the height of the arrowhead.Defaults to4mm.arrow_body_heightgrid::unit()object giving the height of the body of the arrow.Defaults to3mm.DetailsThis geom draws genes as arrows along a horizontal line representing the molecule.The start and end locations of the gene are expressed with the xmin and xmax aesthetics,while the molecule can be specified with the y aesthetic.Optionally,an additional forward aesthetic can be used to reverse the orientation of some or all genes from that implied by xmin and xmax.Unless the plot is faceted with a free x scale,all the molecules will share a common x axis.This means that if the locations are very different across different molecules,the genes might appear very small and squished together with a lot of unnecessary empty space.To get around this,eitherfacet the plot with scales="free_x",or normalise the gene locations if their exact locations are not important.See make_alignment_dummies()for a method to align genes between molecules.Aesthetics•xmin,xmax(start and end of the gene;will be used to determine gene orientation)•y(molecule)•forward(if any value that is not TRUE,or coercible to TRUE,the gene arrow will be drawn in the opposite direction to that determined by xmin and xmax)•alpha•colour•fill•linetype•sizeSee Alsotheme_genes(),make_alignment_dummies(),geom_gene_label()Examplesggplot2::ggplot(example_genes,ggplot2::aes(xmin=start,xmax=end,y=molecule,fill=gene))+ geom_gene_arrow()+ggplot2::facet_wrap(~molecule,scales="free")geom_gene_label A’ggplot2’geom to add text labels to gene arrowsDescriptiongeom_gene_label()can be used to add a text label to genes drawn with geom_gene_arrow().Usagegeom_gene_label(mapping=NULL,data=NULL,stat="identity",position="identity",na.rm=FALSE,show.legend=FALSE,inherit.aes=TRUE,padding.x=grid::unit(1,"mm"),padding.y=grid::unit(0.1,"lines"),align="centre",min.size=4,grow=F,reflow=F,height=grid::unit(3,"mm"),...)Argumentsmapping,data,stat,position,na.rm,show.legend,inherit.aes,...Standard geom arguments as for ggplot2::geom_text().padding.x,padding.ygrid::unit()object,giving horizontal or vertical padding around the text.De-faults to1mm and0.1lines respectively.align Where inside the gene to place the text label.Default is’centre’;other options are’left’and’right’.min.size Minimum font size,in points.If provided,text that would need to be shrunk below this size tofit inside the gene arrow will not be drawn.Defaults to4pt.grow If TRUE,text will be grown as well as shrunk tofill the arrow.reflow If TRUE,text will be reflowed(wrapped)to betterfit the arrow.height grid::unit()object giving the maximum height of the text.Defaults to3mm, which is the default height of gene arrows drawn with geom_gene_arrow(). Detailsgeom_gene_label()uses the’ggfittext’package tofit text to genes.All text drawing options available in ggfittext::geom_fit_text()(growing,reflowing,etc.)are also available here.For full details on how these options work,see the documentation for ggfittext::geom_fit_text().Standard’ggplot2’aesthetics for text are supported(see Aesthetics).Aesthetics•xmin,xmax(start and end of the gene;required)•y(molecule;required)•label(the label text;required)•colour•size•alpha•family•fontface•angle10geom_subgene_arrowSee Alsogeom_gene_arrowExamplesggplot2::ggplot(example_genes,ggplot2::aes(xmin=start,xmax=end,y=molecule,fill=gene,label=gene))+geom_gene_arrow()+geom_gene_label()+ggplot2::facet_wrap(~molecule,ncol=1,scales="free")+theme_genes()geom_subgene_arrow A’ggplot2’geom to draw subgene segments of gene arrowsDescriptiongeom_subgene_arrow()draws subgenes segments within gene arrows drawn with geom_gene_arrow(). Usagegeom_subgene_arrow(mapping=NULL,data=NULL,stat="identity",position="identity",na.rm=FALSE,show.legend=NA,inherit.aes=TRUE,arrowhead_width=grid::unit(4,"mm"),arrowhead_height=grid::unit(4,"mm"),arrow_body_height=grid::unit(3,"mm"),...)Argumentsmapping,data,stat,position,na.rm,show.legend,inherit.aes,...As standard for’ggplot2’.arrowhead_widthgrid::unit()object giving the width of the arrowhead.Defaults to4mm.Ifthe gene is drawn smaller than this width,only the arrowhead will be drawn,compressed to the length of the gene.arrowhead_heightgrid::unit()object giving the height of the arrowhead.Defaults to4mm.arrow_body_heightgrid::unit()object giving the height of the body of the arrow.Defaults to3mm.DetailsThe start and end locations of the subgene are given with the xsubmin and xsubmax aesthetics.geom_subgene_arrow()requires some information about the’parent’gene,provided with thesame aesthetics used for geom_gene_arrow():start and end locations of the’parent’gene withthe xmin and xmax aesthetics,the molecule with the y aesthetic,and optionally the direction withthe forward aesthetic.If the geometry of the parent gene has been changed with arrowhead_width,arrowhead_height or arrow_body_height,identical parameters should be given to geom_subgene_arrow().Aesthetics•xmin,xmax(start and end of the gene;will be used to determine gene orientation)•xsubmin,xsubmax(start and end of subgene segment).Should be consistent with xmin/xmax•y(molecule)•forward(if FALSE,or coercible to FALSE,the gene arrow will be drawn in the oppositedirection to that determined by xmin and xmax)•alpha•colour•fill•linetype•sizeSee Alsogeom_gene_arrow(),geom_subgene_label()Examplesggplot2::ggplot(example_genes,ggplot2::aes(xmin=start,xmax=end,y=molecule))+geom_gene_arrow()+geom_subgene_arrow(data=example_subgenes,ggplot2::aes(xmin=start,xmax=end,xsubmin=from,xsubmax=to,y=molecule,fill=gene))+ggplot2::facet_wrap(~molecule,scales="free")geom_subgene_label A’ggplot2’geom to add text labels to subgenesDescriptiongeom_subgene_label()can be used to add a text label to subgenes drawn with geom_subgene_arrow().Usagegeom_subgene_label(mapping=NULL,data=NULL,stat="identity",position="identity",na.rm=FALSE,show.legend=FALSE,inherit.aes=TRUE,padding.x=grid::unit(1,"mm"),padding.y=grid::unit(0.1,"lines"),align="centre",min.size=4,grow=F,reflow=F,height=grid::unit(3,"mm"),...)Argumentsmapping,data,stat,position,na.rm,show.legend,inherit.aes,...Standard geom arguments as for ggplot2::geom_text().padding.x,padding.ygrid::unit()object,giving horizontal or vertical padding around the text.De-faults to1mm and0.1lines respectively.align Where inside the subgene to place the text label.Default is’centre’;other op-tions are’left’and’right’.min.size Minimum font size,in points.If provided,text that would need to be shrunk below this size tofit inside the subgene will not be drawn.Defaults to4pt.grow If TRUE,text will be grown as well as shrunk tofill the subgene.reflow If TRUE,text will be reflowed(wrapped)to betterfit the subgene.height grid::unit()object giving the maximum height of the text.Defaults to3mm, which is the default height of gene arrows(and therefore of subgenes)drawnwith geom_gene_arrow().Detailsgeom_subgene_label()uses the’ggfittext’package tofit text to genes.All text drawing options available in ggfittext::geom_fit_text()(growing,reflowing,etc.)are also available here.For full details on how these options work,see the documentation for ggfittext::geom_fit_text().Standard’ggplot2’aesthetics for text are supported(see Aesthetics.)Aesthetics•xsubmin,xsubmax(start and end of the subgene;required)make_alignment_dummies13•y(molecule;required)•colour•size•alpha•family•fontface•anglemake_alignment_dummiesPrepare dummy data to visually align a single gene across facetedmoleculesDescriptionmake_alignment_dummies()helps you to visually align genes across molecules that have been faceted with a free x scale.The output of this function is a data frame of dummy genes.If these dummy genes are added to a’ggplot2’plot with ggplot::geom_blank(),they will extend the x axis range in such a way that the start or end of a selected gene is visually aligned across the facets. Usagemake_alignment_dummies(data,mapping,on,side="left")Argumentsdata Data frame of genes.This is almost certainly the same data frame that will later be passed to ggplot2::ggplot().mapping Aesthetic mapping,created with ggplot2::aes().Must contain the following aesthetics:xmin,xmax,y,and id(a unique identifier for each gene).on Name of gene to be visually aligned across facets.This gene must be present in ’data’,in the column mapped to the id aesthetic.side Should the visual alignment be of the’left’(default)or’right’side of the gene? Examplesdummies<-make_alignment_dummies(example_genes,ggplot2::aes(xmin=start,xmax=end,y=molecule,id=gene),on="genE")ggplot2::ggplot(example_genes,ggplot2::aes(xmin=start,xmax=end,y=molecule,fill=gene))+geom_gene_arrow()+ggplot2::geom_blank(data=dummies)+ggplot2::facet_wrap(~molecule,scales="free",ncol=1)14theme_genes theme_genes A’ggplot2’theme for drawing gene mapsDescriptionThis theme removes extraneous plot elements for drawing an’arrows-on-a-string’style gene map in’ggplot2’.theme_genes_flipped()is like theme_genes(),but forflipped coordinates. Usagetheme_genes()theme_genes_flipped()DetailsThis theme removes strip text(the text that labels facets when you use ggplot2::facet_wrap()or ggplot::facet_grid()).This makes it easier to draw molecules on different x scales by setting the y aesthetic to the molecule,then faceting with facet_grid(~molecule,scales="free"). See Alsogeom_gene_arrow()Examplesggplot2::ggplot(example_genes,ggplot2::aes(xmin=start,xmax=end,y=molecule,fill=gene))+ geom_gene_arrow()+ggplot2::facet_wrap(~molecule,scales="free")+theme_genes()Index∗datasetsexample_dummies,2example_features,2example_genes,3example_dummies,2example_features,2example_genes,3example_subgenes(example_genes),3geom_feature,4geom_feature(),6geom_feature_label,5geom_feature_label(),5geom_gene_arrow,7geom_gene_arrow(),11,14geom_gene_label,8geom_gene_label(),8geom_subgene_arrow,10geom_subgene_label,11geom_subgene_label(),11make_alignment_dummies,13make_alignment_dummies(),8theme_genes,14theme_genes(),8theme_genes_flipped(theme_genes),1415。
org-mode⼊门教程org-mode ⼊门教程By Z.H. Fu切问录org-mode ⼊门教程 org-mode是Emacs提供的⼀个强⼤的编辑模式，可以⽤于做会议笔记以及制作各种待办事项（GDT）。
其语法类似于Markdown但是提供了⽐Markdown更多的操作，再加上Emacs强⼤的编辑功能，能给笔记增加很多动态的操作（能纯⽂本上实现折叠、展开、树状视图、表格求和、求代码运⾏结果等功能），可以说org-mode是最强⼤的标记语⾔。
⽽org-mode的强⼤，也导致了他⽐markdown更加复杂，需要花些时间来练习，本⽂选出了org-mode最强⼤、实⽤的功能，进⾏最简单的介绍，下⾯介绍org-mode的使⽤⽅法。
安装配置 org-mode功能基本⽐较完善，不需要更多的配置，但是org模式下默认没有⾃动换⾏的功能，我们在.emacs⽂件⾥⾯添加如下代码，实现⾃动换⾏：(add-hook 'org-mode-hook (lambda () (setq truncate-lines nil)))实例教程 以下分别讲解org-mode下⼏个实⽤的功能，更完整的教程可以参考。
下⾯⼀步⼀步完成我们的org⽂件。
（本教程中我们定义C-x表⽰按Ctrl+x，M+x标识Alt+x，S+x代表Shift+x，这也是Emacs的标准定义）新建⽂件1) 打开Emacs2) 输⼊C-x C-f ～/test/注意⽂件后缀名为org，该命令新建了⼀个名为的⽂件。
新建完⽂件后，我们就可以输⼊相应的内容了。
以下是org-mode语法的具体介绍。
章节 org-mode⽤*标识章节，⼀个*代表⼀级标题，两个*代表两级标题，以此类推。
在Emacs中输⼊以下内容：* 标题⼀** 标题⼆ 注意型号后⾯有空格。
可以发现，不同层级标题的颜⾊是不⼀样的。
按Alt加左右键能够升降标题的层级。
⼀些常⽤快捷键如下：S+Tab展开、折叠所有章节Tab对光标所在章节进⾏展开、折叠M+left/right升级/降级标题列表 列表是⽂本中⼀个⽐较常⽤的元素，可以列出各种待完成的事项等。
Package‘bigmemory.sri’November9,2022Type PackageTitle A Shared Resource Interface for Bigmemory Project PackagesVersion0.1.6Author Michael J.KaneMaintainer Michael J.Kane<**************************>Contact Michael J.Kane<**************************>Description A shared resource interface for the bigmemory and synchronicity packages.Encoding UTF-8Language en-USLicense LGPL-3|Apache License2.0Enhances bigmemoryImports methodsRoxygenNote7.2.1NeedsCompilation noRepository CRANDate/Publication2022-11-0914:50:05UTCR topics documented:bigmemory.sri-package (2)attach.resource (2)describe (3)Index512attach.resource bigmemory.sri-package A Shared Resource Interface for Bigmemory Project PackagesDescriptionA shared resource interface for the bigmemory and synchronicity packages.DetailsPackage:bigmemory.sriType:PackageVersion:0.1.4License:LGPL-3|Apache License2.0Both the bigmemory and synchronicity package use a common interface for using a computer’s shared resources.Previously the package checked to see if the other package was loaded and if it was not the interface was loaded.However,this approach relied on a.Internal call in the zzz.R file.However,due to recent changes in CRAN policy this approach has become verboten.The bigmemory.sri package was created to handle this interface dependency without violating CRAN package guidelinesAuthor(s)Michael J.KaneMaintainer:Michael J.Kane<**************************>See Alsobigmemoryattach.resource Create an Object that Makes Use of a Shared ResourceDescriptionThis generic function should be used to attach to a system-wide shared resource on a computer.It is used by other packages.Usageattach.resource(obj,...)Argumentsobj a descriptor object describing the location and type of a shared resource....other information needed for object-specific attaching.ValueAn R object that makes use of a share resource.#Create a concrete function.setMethod("at-tach.resource",signature(x="NULL"),function(obj,...)NULL)#Describe it attach.resource(NULL)describe Create a Description of a Shared ResourceDescriptionThis generic function should be used for creating a description of a shared resource and is used in conjunction with attache.resource to utilize shared resources from an R session.Usagedescribe(x)Argumentsx the object to create the descriptor for.ValueA user-defined description of a shared resource.See Also[bigmemory.sri::attach.resource()]Examples#Create a concrete function.setMethod("describe",signature(x="list"),function(x){print(x$value)})#Create an object to describe.tst=list(loc="in_ram_not_shared",value="hello world") #Describe itdescribe(tst)Indexattach.resource,2bigmemory,2bigmemory.sri(bigmemory.sri-package),2 bigmemory.sri-package,2describe,35。
