link.map.default(wgaim)
link.map.default()所属R语言包：wgaim
Plot a genetic linkage map with QTL for multiple traits
绘制遗传图谱与多性状QTL
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Neatly plots the genetic linkage map with marker locations, marker names and highlights QTL's with their associated flanking markers for multiple traits obtained from a list of wgaim fits.
整齐地绘制遗传连锁图的标记位置，标记名称和亮点QTL从列表中的wgaim一刀切的多性状相关的标记。
用法----------Usage----------
## Default S3 method:[默认方法]
link.map(object, intervalObj, chr, max.dist, marker.names
= "markers", list.col = list(q.col = rainbow(length(object)),
m.col = "red", t.col = rainbow(length(object))), list.cex =
list(m.cex = 0.6, t.cex = 0.6), trait.labels = NULL, tick = FALSE, ...)
参数----------Arguments----------
参数：object
a list object with elements inheriting the class "wgaim"
一个列表对象的元素继承的类“wgaim。”
参数：intervalObj
object of class "cross" or "interval"
类的对象“cross”或“interval”
参数：chr
character string naming the subset of chromosomes to plot
字符串命名的染色体子集图
参数：max.dist
a numerical value in cM determining the distance the genetic map should be subsetted by
cM的确定的距离的遗传图中的数值应子集
参数：marker.names
a character string naming the type of marker information to plot. If "dist" then distances names plotted alongside each chromosome on the left. If "markers" then marker names are plotted instead. Defaults to "markers".
一个字符串，命名类型的标记信息绘制。如果“dist”，然后绘制距离名称沿着每一条染色体上的左边。如果“markers”标记名称，而不是被绘制。默认“markers”。
参数：list.col
named list of colors used to highlight the QTL regions and their flanking markers. q.col is the colors of the QTL regions (defaults to rainbow(n) where n is the length of object). m.col is the color the flanking markers. t.col is the color of the trait names used in each model (defaults to the same color as the QTL regions). See par for color options
使用的颜色突出的的QTL区域和他们的侧翼标记的命名列表。 q.col的QTL区域的颜色（默认为rainbow(n)其中n的长度object的）。 m.col的颜色标记。 t.col是每个模型中使用的名称（默认为相同颜色的QTL区域）的性状的颜色。见par颜色选项
参数：list.cex
a named list object containing the character expansion factors for the marker names m.cex and the trait labels t.cex
一个名为list的对象，它包含的字符扩展的标记因素命名为m.cex和特质标签t.cex
参数：trait.labels
character string naming the trait used in the model object, defaults to the names of the traits used in each model.
字符串命名的特征模型中的对象，使用默认的名字在每一个模型的特点。
参数：tick
logical value. If TRUE then an axis with tick marks are generated for the chromosome names
逻辑值。如果TRUE然后一个轴的刻度线产生的染色体名
参数：...
arguments passed to "plot" to set up the plot region. Arguments may also be passed to "text" for the manipulation of the marker names
参数传递“plot”设置的图区域。参数也被传递给“text”的标记名称的操纵
Details
详细信息----------Details----------
This plotting procedure is a wrapper for link.map.wgaim and displays QTL for multiple traits obtained from a list of models given by object. Alternative labels for the traits can be given, in model order, using trait.labels.
绘制过程是一个包装link.map.wgaim和显示模型的object从列表中获得的多性状QTL的。的特点，可替代标签，在模型的阶数，使用trait.labels。
Color specific highligting of the QTL is also available using clist. This differs slightly from link.map.wgaim. Here the q.col and t.col should be given a set of colors equal to the length of object. Let n be the length of object. Then if q.col is NULL or length of q.col is not equal to n then it defaults to rainbow(n). If <CITE>t.col</CITE> is NULL or length of t.col is not equal to n or 1 then it defaults to the colors of q.col. Examples of different color combinations are given below.
也可以使用clist颜色特定highligting的QTL。这略有不同link.map.wgaim。这里的q.col和t.col应的颜色等于的长度object的一组。让我们n是长度object。然后，如果q.col是NULL或q.col是不是等于n，则默认为rainbow(n)的长度。如果<CITE> t.col </ CITE>NULL或t.col不等于n或1，那么它默认的颜色q.col长度。不同的颜色组合的例子在下面给出。
The list.cex argument can be used to manipulate the character expansion of the marker names using m.cex or the character expansion of the trait.labels using t.cex. If a set of "marker" analyses has been performed then pch is used to plot a symbol at the location of the QTL. This character can be changed using the usual arguments such as pch or cex that are passed through the usual ... argument.
可用于操纵字符扩展的标记名称使用list.cex或字符扩展的m.cex使用trait.labelst.cex参数。如果已经执行“标记”的一组分析然后pch的QTL的位置时被使用来绘制一个符号。该字符可以使用常规的参数如pch或cex通常通过改变...的说法。
值----------Value----------
For a set of "interval" analyses, the genetic linkage map is plotted with shaded QTL regions and highlighted flanking markers. For a set of "marker" analyses, symbols are placed at the QTL locations and the markers are highlighted.
对于一组的“间隔”的分析，遗传连锁图谱的绘制阴影的QTL区域和突出标记。如果在“标记”分析的一组中，符号的QTL的位置放置在突出显示的标记。
（作者）----------Author(s)----------
Julian Taylor
参考文献----------References----------
Bi-Parental Populations Using Linear Mixed Models. Journal of Statistical Software, 40(7), 1-18. URL http://www.jstatsoft.org/v40/i07/.
参见----------See Also----------
link.map.cross, link.map.wgaim
link.map.cross，link.map.wgaim
实例----------Examples----------
## Not run: [＃不运行：]
## fit wgaim models[＃适合wgaim模型。]
zn.qtl <- wgaim(zn.fm, phenoData = zinc, intervalObj = raccasS,
merge.by = "id", trace = "trace.txt", na.method.X = "include")
zn.qtlS <- wgaim(zn.fmS, phenoData = zinc, intervalObj = raccasS,
merge.by = "id", trace = "trace.txt", na.method.X = "include")
## plot QTL intervals[＃图QTL的时间间隔]
# matching rainbow QTL color and trait names, red flanking markers[匹配彩虹QTL的颜色和性状的名称，红色标记]
# (default) and gray background markers.[（默认）和灰色的背景标志。]
link.map(list(zn.qtl,zn.qtlS), raccas, col = "gray")
# rainbow QTL color and black trait names, red flanking markers[的彩虹的QTL颜色和黑色的特质名称，红色标记]
# (default) and gray background markers.[（默认）和灰色的背景标志。]
link.map(list(zn.qtl,zn.qtlS), raccas, list.col = list(t.col =
"black", m.col = "red"), col = "gray")
# monochromatic plot: gray QTLs, black trait names, black flanking[单色的图：灰色的QTL，黑色性状的名字，黑色的侧翼]
# markers and gray background markers[标记和灰色的背景标志]
link.map(list(zn.qtl,zn.qtlS), raccas, list.col = list(q.col =
rep(gray(0.8), 2), t.col = "black", mcol = "black"), col = "gray")
## 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 2012-10-1 21:04:10
