plotRangesLinkedToData(ggbio)
plotRangesLinkedToData()所属R语言包：ggbio
Plot Ranges Linked with Data
图范围与数据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Plot GRanges object structure and linked to a even spaced paralell coordinates plot which represting the data in elementeMetadata.
积农庄对象的结构和挂甚至的间隔paralell坐标图其中represting在elementeMetadata数据的。
用法----------Usage----------
plotRangesLinkedToData(data, stat.col, stat.label, ..., annotation = list(),
width.ratio = 0.8,
heights = c(400, 100, 100, rep(300, length(annotation))))
参数----------Arguments----------
参数：data
GRanges object with a DataFrame as elementMetadata.
农庄反对与为elementMetadata DataFrame。
参数：stat.col
integer (variable position starting in DataFrame of data, start from 1) or strings (variable names) which indicate the column names.
整数（变量在数据DataFrame的立场出发，从1）或字符串（变量名）表示列名。
参数：stat.label
Labels of the columns, if missing, use stat.col.
列的标签，如果缺少，使用stat.col。
参数：...
Parameters passed to qplot.
参数传递qplot。
参数：annotation
A list of ggplot object.
ggplot对象名单。
参数：width.ratio
Control the segment length of statistic layer.
控制统计层段的长度。
参数：heights
Heights of each track.
每首曲目的高地。
Details
详情----------Details----------
Inspired by some graphics produced in some other packages, for example in package DEXseq, the author provides graphics with gene models and linked to an even spaced statistics summary. This is useful because we always plot everything along the genomic coordinates, but genomic features like exons are not evenly distributed, so we could actually treat the statistics associated with exons like categorical data, and show them as "Paralell Coordinates Plots". This is one special layout which represent the data in a nice manner and also keep the genomic structure information. With abliity of tracks, it's possible to generate such type of a graphic along with other annotations.
其他一些包中产生了一些图形的启发，例如包DEXseq，笔者提供与基因模型的图形，甚至间隔的统计汇总。这是有用的，因为我们总是沿基因组坐标绘制一切，但像外显子的基因功能不是均匀分布的，所以我们实际上可以治疗像分类数据外显子相关的统计数字，显示为“Paralell坐标图”。这是一个特殊的布局代表的数据，在一个很好的方式，并保持基因组的结构信息。随着tracksabliity，它可能生成这类图形，以及与其他注解。
The data we want is a normal GRanges object, and make sure the intervals are not overlaped with each other(currently), and you may have multiple columns which store the statistics for multiple samples, then we produce the graphic we introduced above and users could pass other annotation track in the function which will be shown below the main linked track.
我们想要的数据是正常的GRanges对象，并确保间隔不与对方（目前）overlaped，你可能有多个列存储多个样本的统计，那么我们生产的图形，我们介绍上面和用户可以通过在其他注释功能将显示以下主要挂钩轨道轨道。
The reason you need to pass annotation into the function instead of binding them by tracks later is because binding manually with annotation tracks is tricky and this function doesn't return a ggplot object.
究其原因，你需要传递到函数的注释，而不是他们结合：tracks后来是因为绑定与注解轨道手动是棘手的，这个函数并不返回一个ggplot对象。
值----------Value----------
return a frame grob; side-effect (plotting) if plot=T.
返回一帧GROB;副作用（策划）如果图= T
作者（S）----------Author(s)----------
Tengfei Yin
举例----------Examples----------
## Not run: [＃无法运行：]
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
data(genesymbol)
txdb <- Hsapiens_UCSC_hg19_knownGene_TxDb
model <- exonsBy(txdb, by = "tx")
model17 <- subsetByOverlaps(model, genesymbol["RBM17"])
exons <- exons(txdb)
exon17 <- subsetByOverlaps(exons, genesymbol["RBM17"])
## reduce to make sure there is no overlap[＃减少，以确保没有重叠]
## just for example[例如＃刚]
exon.new <- reduce(exon17)
## suppose[＃假设]
values(exon.new)$sample1 <- rnorm(length(exon.new), 10, 3)
values(exon.new)$sample2 <- rnorm(length(exon.new), 10, 10)
values(exon.new)$score <- rnorm(length(exon.new))
plotRangesLinkedToData(exon.new, stat.col = c("sample1", "sample2"))
plotRangesLinkedToData(exon.new, stat.col = 1:2)
plotRangesLinkedToData(exon.new, stat.col = 1:2, annotation = list(p))
## End(Not run)[＃结束（不运行）]
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 2012-2-25 19:44:56
