snp.plotter(snp.plotter)
snp.plotter()所属R语言包：snp.plotter
SNP/haplotype association p-value and linkage disequilibrium plotter
SNP /单体型关联的p值和连锁不平衡绘图仪
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Creates plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple set of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either PDF/EPS files.
创建图的p-值采用单的SNP和/或单倍型数据。包的主要功能包括选项，以显示一个连锁不平衡（LD）的图和结果同时绘制多个组的能力。图可以创建使用全球和/或个别单倍型的p值与单个SNP的p值。图像中创建PDF / EPS文件。
用法----------Usage----------
PVAL.THRESHOLD = 1,
USE.GBL.PVAL = TRUE,
SYMBOLS = NA,
SAMPLE.LABELS = NULL,
LAB.Y = "log",
DISP.HAP = FALSE,
DISP.SNP = TRUE,
DISP.COLOR.BAR = TRUE,
DISP.PHYS.DIST = TRUE,
DISP.LEGEND = TRUE,
DISP.MARKER.LINES = TRUE,
DISP.LDMAP = FALSE,
DISP.TYPE = "symbol",
DISP.MULT.LAB.X = FALSE,
DISP.SNP.NAMES = TRUE,
DISP.CONNECTING.LINES = TRUE,
LD.TYPE = "dprime",
LD.COLOR.SCHEME = "heat",
USE.COLORS = TRUE,
COLOR.LIST = NULL,
PALETTE.FILE = NULL,
IMAGE.TITLE = NULL,
IMAGE.NAME = "snp.plotter",
IMAGE.TYPE = "pdf",
IMAGE.SIZE = 3.5,
CONNECTING.LINES.FACTOR = 1,
CONNECTING.LINES.ADJ = 0,
CONNECTING.LINES.VERT.ADJ = -1,
CONNECTING.LINES.FLEX = 0,
SNP.FILE = NULL,
HAP.FILE = NULL,
GENOTYPE.FILE = NULL,
FONT.FACTOR = NULL,
SYMBOL.FACTOR = NULL,
config.file = NULL
)
参数----------Arguments----------
参数：config.file
Name of a configuration file for snp.plotter parameters in the form ATTRIBUTE=value. This option can be used in place of specifying options at the R command line.
为snp.plotter参数的形式属性值的配置文件的名称。此选项可用于代替在R命令行中指定的选项。
参数：SNP.FILE
Tab-delimited input file containing p-values for single SNPs (see note below). The contents of each SNP.FILE includes four necessary columns ASSOC, SNP.NAME, LOC, and SS.PVAL corresponding to positive or negative association (indicating susceptibility or protective alleles), a SNP label, the location, and a p-value for each SNP. SNP labels cannot start with numbers. Example: "s1.txt,s2.txt,s3.txt" MANDATORY
制表符分隔的输入文件，其中包含的p值单一的单核苷酸多态性（看到下面的注释）。每个SNP.FILE的内容包括四个必要列ASSOC，SNP.NAME，LOC，和对应的正面或负面的联想（表示易感性或保护等位基因），SNP标签的位置，和一个p值SS.PVAL每个SNP。 SNP标签不能以数字开头。例如：“s1.txt，s2.txt，s3.txt”强制性
参数：HAP.FILE
Tab-delimited input file containing p-values for haplotypes (see note below). The contents of each HAP.FILE includes three necessary columns ASSOC, G.PVAL, and I.PVAL followed by a set of columnns of SNPs with corresponding haplotypes. Haplotypes are presented in a step-wise fashion with the major allele given as 1 and the minor allele as 2; haplotype variants for a set of SNPs should be grouped. SNP labels in HAP.FILE must be the same as in SNP.FILE, and only SNPs with corresponding haplotypes need to be included. Example: "h1.txt,h2.txt,h3.txt" OPTIONAL
制表符分隔的输入文件，其中包含的p值的单倍型（看到下面的注释）。每个HAP.FILE的内容包括三个必要的列ASSOC，G.PVAL的，和I.PVAL由一组的SNP位点与相应的单倍型columnns。在一阶梯状的方式与主要等位基因为1和2的次要等位基因的单倍型;应分组为一组的单核苷酸多态性的单倍型的变种。 SNP标签在HAP.FILE必须是相同的如SNP.FILE，和只有单核苷酸多态性与相应的单倍型的需要被包含。例如：“h1.txt，h2.txt，h3.txt”OPTIONAL
参数：GENOTYPE.FILE
Tab-delimited input file containing genotypes as a PED file with 6 columns preceding the genotype data: family ID, individual ID, father ID, mother ID, sex, and affection status; these coloums are not used in the creation of the LD plot. This file is used for calculating D' or r-squared values for the LD heatmap plot. Only one LD plot can be shown (see note below). OPTIONAL
制表符分隔的输入文件，包含6列前的基因型数据：家庭ID，个人ID，父ID，母亲ID，性别，和感情状态作为一个的PED文件与基因型;不使用这些coloums在LD图的创作。这个文件是用来计算D或R-平方值的LD热图图。只有一个LD图可以证明（见下文附注）。可选的
参数：EVEN.SPACED
Logical. Should the p-values be displayed at even spacing or at genetic map distances?
逻辑。应的p值显示在均匀间距或在遗传图谱距离？
参数：USE.GBL.PVAL
Logical. Use global haplotype p-values (as opposed to individual p-values)? Unfilled symbols connected by solid lines are used to indicate global haplotype p-values, default symbol: circle. Unfilled and filled symbols are used to indicate alleles 1 and 2, respectively connected by solid lines and dashed lines for positive and negative association (indicating susceptibility or protective haplotypes) when using individual haplotype p-values.
逻辑。使用全局单倍型的p值（而不是单独的p-值）？用实线连接的未填充的符号是用来表示全球单倍型的p值，默认的符号：圆。未加填料的和填充的符号用于指示等位基因1和2，分别由实线和虚线为正和负关联（表示的易感性或保护的单倍型）连接时，使用单独的单倍型的p值。
参数：DISP.HAP
Logical. Display haplotype p-values?
逻辑。显示单倍型的p值？
参数：DISP.SNP
Logical. Display single SNP p-values?
逻辑。显示单个SNP的p值吗？
参数：DISP.LDMAP
Logical. Display the LD heatmap?
逻辑。显示的LD热图？
参数：DISP.PHYS.DIST
Logical. Display the range of the X-scale?
逻辑。显示的范围内的X-尺度？
参数：DISP.LEGEND
Logical. Display a legend with sample labels and corresponding symbols?
逻辑。显示图例样品标签和相应的符号？
参数：DISP.COLOR.BAR
Logical. Display bar showing colors and corresponding values of LD plot?
逻辑。显示栏显示的颜色和相应的值LD图？
参数：DISP.TYPE
Options: "symbol"
选项：“符号”
参数：DISP.MULT.LAB.X
Logical. Display evenly spaced X-axis tick-labels; up to 5 labels are shown.
逻辑。显示均匀分布的X-轴刻度标签的产品;多达5标签显示。
参数：DISP.MARKER.LINES
Logical. Display lines at p-value thresholds of 0.05, 0.01, 0.001, etc.
逻辑。 p值阈值0.05，0.01，0.001等的显示行
参数：DISP.SNP.NAMES
Logical. Display the names of SNPs on a plot.
逻辑。在一个图上显示的名称的单核苷酸多态性。
参数：DISP.CONNECTING.LINES
Logical. Display connecting lines from p-value plot to LD map.
逻辑。显示连接线从P-值图LD图。
参数：USE.COLORS
Logical. Restrict LD heatmap colors and default symbol colors to gray-scale
逻辑。限制的LD热图的颜色和默认的符号颜色灰度
参数：COLOR.LIST
List of colors (one for each sample) known to GraphApp (see note below) for displaying p-value symbols. Example: "red,blue,green,black,orange"
颜色列表（每个样品）显示p值的符号已知GraphApp（看到下面的注释）。例：“红，蓝，绿，黑，橙”
参数：SYMBOLS
Options: circle, square, diamond, triangle; Symbols can either be filled or not filled by appending "-fill" e.s., square-fill. NA may be specified. In this case, the SNP.FILE ASSOC column is read and an up-triangle and down-triangle are used to indicate positive and negative association (indicating susceptibility or protective alleles), respectively. Example: "circle,NA,diamond-fill,triangle"
选项：圆形，方形，菱形，三角形符号可以填写或不填追加“补”ES，填方。可以指定不适用。在这种情况下，SNP.FILE ASSOC列被读取，是用来表示正和负的关联（表示易感性或保护等位基因），分别向上三角形和向下三角形。例如：“圆，三角形，钻石填充NA”
参数：PALETTE.FILE
Colors are hexidecimal HTML color codes; one color per line. OPTIONAL
颜色是十六进制HTML颜色代码，每行一个颜色。可选的
参数：SAMPLE.LABELS
Labels for each sample. Example: "d-cc,d2-cc,d1-fam"
对每个样品的标签。例如：“D-D2-CC，CC，D1-FAM”
参数：LAB.Y
Options: ln (natural log) or log (log10)
选项为：ln（自然对数）或log（log10）
参数：IMAGE.TYPE
Options: "pdf" or "eps"
选项：“pdf”或“EPS”
参数：IMAGE.TITLE
Title of the image in quotes. Note: Title text may not wrap.
在引号中的图像的标题。注：标题文本不换行。
参数：IMAGE.SIZE
Options: 3.5 or 7. Sizes are in inches and correspond to 1 or 2 columns per printed page.
选项：3.5或7。尺寸都以英寸为单位，并对应于1或2列每张打印页。
参数：IMAGE.NAME
Name of the output file. The correct extension will be appended depending on the value of IMAGE.TYPE
输出文件的名称。正确的扩展名被追加的价值IMAGE.TYPE
参数：PVAL.THRESHOLD
The minimum value of the the Y-scale will be set to this value. Default: 1 (to ignore option).
将被设置为这个值的最小值的Y标尺。默认：1（忽略“选项）。
参数：LD.TYPE
LD metric. Options: "dprime" or "rsquare"
LD的度量。选项：“dprime”或“rsquare”
参数：LD.COLOR.SCHEME
LD heatmap color scheme. Options: heat (red-yellow-white), cm (cyan-magenta), topo (topographical map colors), gray (gray-scale), or custom; custom requires palette file (PALETTE.FILE) to be defined
LD热图的配色方案。选项：热（红，黄，白），厘米（青色，洋红色），地形（地形图的颜色），灰色（灰度），或自定义，定制需要调色板的文件（PALETTE.FILE），被定义
参数：CONNECTING.LINES.FACTOR
Adjusts the length of the connecting lines. Range: 0-2
调节的连接线的长度。范围：0-2
参数：CONNECTING.LINES.ADJ
Can be used to adjust the position of connecting lines in relation to SNP names. Negative values shift the connecting lines to the left and positive values shift the lines to the right. Range: 0-1
可以用来调整到SNP名称有关的连接线的位置。负的值转移的连接线的左侧和正面的价值观转移线向右侧。范围：0-1
参数：CONNECTING.LINES.VERT.ADJ
Can be used to vertically adjust the position of connecting lines in relation to SNP names. More negative value shift the connecting lines down. Range: -0.5-0
可用于垂直调整到SNP名称有关的连接线的位置。更多负值连接线转移。范围：-0.5-0
参数：CONNECTING.LINES.FLEX
Adjusts the spread of the connecting lines. Range: 0-2
调整连接线传播。范围：0-2
参数：SYMBOL.FACTOR
Scaling value for symbols. Larger values are generate larger symbols. Range: 0-1
定标值的符号。较大的值产生较大的符号。范围：0-1
参数：FONT.FACTOR
Scaling value for SNP names. Larger values are generate larger SNP names. Range: 0-1
缩放值为SNP名称。较大的值产生较大的SNP名称。范围：0-1
Details
详细信息----------Details----------
snp.plotter produces publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot below the p-value plot using either the r-squared or D' LD metric with a user-specified LD heatmap color scheme, setting the X-axis to equal spacing or to use the physical SNP map, and specification of plot labels, colors and symbols for desplaying p-values. A major strength of the package is that it can plot multiple set of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. The package provides a simple way to convey both association and LD information in a single appealing graphic and requires virtually no knowledge of the R programming language. Code to create the LD map was modified from the
snp.plotter发布，采用单的SNP和/或单倍型数据的p-值的优质图。的软件包的主要功能包括选项，以显示下面的p-值图使用的R-平方或DLD度量的图与用户指定的LD热图的配色方案，设置X轴等于一个连锁不平衡（LD）间距或使用物理SNP图谱，和规格的绘图标签，颜色和符号desplaying p-值。的包的主要优势是，它可以绘制多个结果集同时。图可以创建使用全球和/或个别单倍型的p值与单个SNP的p值。该软件包提供了一个简单的方式来传达关联和LD信息在一个单一的有吸引力的图形和要求几乎没有了R编程语言的知识。修改代码创建LD图
值----------Value----------
A list containing two items: config.var and gbl.var, which includes the values of all significant variables used by snp.plotter
一个列表，其中包含两个项目：config.var和gbl.var，其中包括使用snp.plotter的所有重要变量的值
注意----------Note----------
Configuration FilesDue to the large number of parameters implemented for flexibility, it is suggested that snp.plotter be run using the config.file argument.
配置FilesDue大量的参数实现的灵活性，，建议snp.plotter的运行使用config.file参数。
Example DatasetsExamples of SNP.FILE, HAP.FILE, GENOTYPE.FILE, and configuration files are provided at http://cbdb.nimh.nih.gov/~kristin/snp.plotter.html with further explanation on the file formats.
例DatasetsExamples SNP.FILE，HAP.FILE，GENOTYPE.FILE和配置文件，在http://cbdb.nimh.nih.gov/~克里斯汀/ snp.plotter.html的进一步解释的文件格式。
ListsComma delimited lists (SNP.FILE, HAP.FILE, COLOR.LIST, SYMBOLS, etc) should not have spaces between entries. If using the config.file argument, these lists should not have quotations in the configuration file. Example: "red,blue,green,black,orange"
ListsComma分隔的列表（SNP.FILE，HAP.FILE，COLOR.LIST，符号等）的条目之间不能有空格。如果使用config.file参数，这些名单应该在配置文件中没有报价。例：“红，蓝，绿，黑，橙”
ColorsCOLOR.LIST colors are limited to those known to GraphApp. A short list can be found at http://en.wikipedia.org/wiki/X11.color.names; the complete list is located in the R source code file
ColorsCOLOR.LIST颜色仅限那些已知GraphApp。 ，可以在http://en.wikipedia.org/wiki/X11.color.names;在R源代码文件的完整列表位于短名单
PalettesPALETTE.FILE colors are hexidecimal HTML color codes http://en.wikipedia.org/wiki/X11.color.names. The first and last colors correspond to the lowest and highest value of the chosen LD metric, respectively. One color per line.
PalettesPALETTE.FILE颜色的十六进制HTML颜色代码http://en.wikipedia.org/wiki/X11.color.names。第一个和最后一个颜色的选择的LD度量的最低值和最高值，分别对应。每一种颜色线。
PDFsThe error "unable to start device pdf" may occur when attempting to overwrite an open PDF document.
PDFsThe错误“无法启动设备概览”在试图覆盖打开的PDF文档时可能会出现。
P-valuesA p-value of 1 or NA can be used in SNP.FILE to prevent displaying information about a single SNP
P-值a p值为1或NA可以用在SNP.FILE的，以防止显示信息的一个单一的SNP的
Number of Datasetssnp.plotter handles 10 set of results, but provides default values for only 5 set of results
数Datasetssnp.plotter处理10个结果集，但只有5的结果集提供了默认值
File InputAll input files should be placed in the same directory </ul>
文件InputAll输入文件应放置在同一个目录</ ul>
（作者）----------Author(s)----------
Augustin Luna <a href="mailto:augustin.luna@mail.nih.gov">augustin.luna@mail.nih.gov</a>, Kristin K. Nicodemus <a href="mailto:kristin.nicodemus@well.ox.ac.uk">kristin.nicodemus@well.ox.ac.uk</a>, <a href="mailto:nicodemusk@mail.nih.gov">nicodemusk@mail.nih.gov</a>. Website: <a href="http://cbdb.nimh.nih.gov/~kristin/snp.plotter.html">http://cbdb.nimh.nih.gov/~kristin/snp.plotter.html</a>
实例----------Examples----------
## Not run: [＃不运行：]
snp.plotter(config.file = "config.txt")
## End(Not run)[＃（不执行）]
## Not run: [＃不运行：]
snp.plotter(EVEN.SPACED = FALSE,
PVAL.THRESHOLD = 1,
USE.GBL.PVAL = TRUE,
SYMBOLS = NA,
SAMPLE.LABELS = NULL,
LAB.Y = log,
DISP.HAP = FALSE,
DISP.SNP = TRUE,
DISP.COLOR.BAR = TRUE,
DISP.PHYS.DIST = TRUE,
DISP.LEGEND = TRUE,
DISP.MARKER.LINES = TRUE,
DISP.LDMAP = FALSE,
DISP.TYPE = "symbol",
DISP.MULT.LAB.X = FALSE,
DISP.SNP.NAMES = TRUE,
DISP.CONNECTING.LINES = TRUE,
LD.TYPE = "dprime",
LD.COLOR.SCHEME = "heat",
USE.COLORS = TRUE,
COLOR.LIST = NULL,
PALETTE.FILE = NULL,
FONT.FACTOR = NA,
IMAGE.TITLE = NULL,
IMAGE.NAME = "snp.plotter",
IMAGE.TYPE = "pdf",
IMAGE.SIZE = 3.5,
CONNECTING.LINES.FACTOR = 1,
CONNECTING.LINES.ADJ = 0,
CONNECTING.LINES.VERT.ADJ = 0,
CONNECTING.LINES.FLEX = 0,
SNP.FILE = NULL,
HAP.FILE = NULL,
GENOTYPE.FILE = NULL,
FONT.FACTOR = NULL,
SYMBOL.FACTOR = NULL,
config.file = NULL
)
## End(Not run)[＃（不执行）]
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-9-30 11:07:07
