plot.peaksDataset(flagme)
plot.peaksDataset()所属R语言包：flagme
Plotting functions for GCMS data objects
GCMS数据对象的绘图功能
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Store the raw data and optionally, information regarding signal peaks for a number of GCMS runs
存储的原始数据，并有选择地，有关信号峰值为GCMS运行数
用法----------Usage----------
.plotpD(object,runs=1:length(object@rawdata),mzind=1:nrow(object@rawdata[[1]]),
mind=NULL,plotSampleLabels=TRUE,calcGlobalMax=FALSE,peakCex = 0.8,plotPeaks=TRUE,
plotPeakBoundaries=FALSE,plotPeakLabels=FALSE,plotMergedPeakLabels=TRUE,mlwd=3,
usePeaks=TRUE,plotAcrossRuns=FALSE,overlap=F,rtrange=NULL,cols=NULL,thin=1,
max.near=median(object@rawrt[[1]]),how.near=50,scale.up=1,...)
.plotpA(object,xlab="Peaks - run 1",ylab="Peaks - run 2",plotMatches=TRUE,matchPch=19,matchLwd=3,
matchCex=.5,matchCol="black",col=colorpanel(50,"black","blue","white"),
breaks=seq(0,1,length=51),...)
.plotcA(object,alignment=1,...)
参数----------Arguments----------
参数：object
a peaksDataset, peaksAlignment or clusterAlignment object.
peaksDataset，peaksAlignment或clusterAlignment对象。
参数：runs
for peaksDataset only: set of run indices to plot
peaksDataset只运行指标设置到图
参数：mzind
for peaksDataset only: set of mass-to-charge indices to sum over (default, all)
peaksDataset只总结（默认情况下，所有的质量负责指数）
参数：mind
for peaksDataset only: matrix of aligned indices
peaksDataset唯一的一致指数矩阵
参数：plotSampleLabels
for peaksDataset only: logical, whether to display sample labels
peaksDataset唯一的逻辑，是否显示样品标签
参数：calcGlobalMax
for peaksDataset only: logical, whether to calculate an overall maximum for scaling
peaksDataset唯一的逻辑，是否计算整体最大缩放
参数：peakCex
character expansion factor for peak labels
高峰标签字符的膨胀系数
参数：plotPeaks
for peaksDataset only: logical, whether to plot hashes for each peak
peaksDataset唯一的逻辑，是否绘制每个峰的哈希
参数：plotPeakBoundaries
for peaksDataset only: logical, whether to display peak boundaries
peaksDataset唯一的逻辑，是否显示高峰的界限
参数：plotPeakLabels
for peaksDataset only: logical, whether to display peak labels
peaksDataset唯一的逻辑，是否显示高峰标签
参数：plotMergedPeakLabels
for peaksDataset only: logical, whether to display 'merged' peak labels
peaksDataset唯一的逻辑，是否显示“合并”高峰标签
参数：mlwd
for peaksDataset only: line width of lines indicating the alignment
peaksDataset只：行表示对齐线的宽度
参数：usePeaks
for peaksDataset only: logical, whether to plot alignment of peaks (otherwise, scans)
peaksDataset唯一的逻辑，是否绘制峰对齐（否则，扫描）
参数：plotAcrossRuns
for peaksDataset only: logical, whether to plot across peaks when unmatched peak is given
peaksDataset唯一的逻辑，是否绘制整个峰无与伦比的高峰时，给出
参数：overlap
for peaksDataset only: logical, whether to plot TIC/XICs overlapping
peaksDataset唯一的逻辑，是否绘制议会/ XICs重叠的
参数：rtrange
for peaksDataset only: vector of length 2 giving start and end of the X-axis
peaksDataset只有向量长度为2 X轴的起始和结束
参数：cols
for peaksDataset only: vector of colours (same length as the length of runs)
peaksDataset只有颜色的向量（如运行长度的长度相同）
参数：thin
for peaksDataset only: when usePeaks=FALSE, plot the alignment lines every thin values
peaksDataset只有当usePeaks=FALSE，对齐线绘制每thin值
参数：max.near
for peaksDataset only: where to look for maximum
peaksDataset只：到哪里寻找最大
参数：how.near
for peaksDataset only: how far away from max.near to look
peaksDataset只有：如何远离max.near看
参数：scale.up
for peaksDataset only: a constant factor to scale the TICs
peaksDataset只有一个常数因子扩展的TICS
参数：plotMatches
for peaksDataset only: logical, whether to plot matches
peaksDataset唯一的逻辑，是否绘制比赛
参数：xlab
for peaksAlignment and clusterAlignment only: x-axis label
peaksAlignment和clusterAlignment只：X轴标签
参数：ylab
for peaksAlignment and clusterAlignment only: y-axis label
peaksAlignment和clusterAlignment只：Y轴标签
参数：matchPch
for peaksAlignment and clusterAlignment only: match plotting character
peaksAlignment和clusterAlignment只匹配绘制字符
参数：matchLwd
for peaksAlignment and clusterAlignment only: match line width
peaksAlignment和clusterAlignment只匹配线宽
参数：matchCex
for peaksAlignment and clusterAlignment only: match character expansion factor
peaksAlignment和clusterAlignment只匹配字符膨胀系数
参数：matchCol
for peaksAlignment and clusterAlignment only: match colour
peaksAlignment和clusterAlignment只匹配颜色
参数：col
for peaksAlignment and clusterAlignment only: vector of colours for colourscale
peaksAlignment和clusterAlignment只有：colourscale颜色矢量
参数：breaks
for peaksAlignment and clusterAlignment only: vector of breaks for colourscale
peaksAlignment和clusterAlignment只为向量colourscale截断
参数：alignment
for peaksAlignment and clusterAlignment only: the set of alignments to plot
peaksAlignment和clusterAlignment唯一的一套路线绘制
参数：...
further arguments passed to the plot or image command
通过进一步的论据plot或image命令
Details
详情----------Details----------
For peakDataset objects, each TIC is scale to the maximum value (as specified by the how.near and max.near values). The many parameters gives considerable flexibility of how the TICs can be visualized.
peakDataset对象，每个议会是规模最大的值（如how.near和max.near值指定）。许多参数如何的TICS可以是可视化提供了相当的灵活性。
For peakAlignment objects, the similarity matrix is plotted and optionally, the set of matching peaks. clusterAlignment objects are just a collection of all pairwise peakAlignment objects.
peakAlignment对象，相似矩阵绘制和可选的匹配峰组。 clusterAlignment对象是所有成对peakAlignment对象的集合。
作者（S）----------Author(s)----------
Mark Robinson
参考文献----------References----------
参见----------See Also----------
plotImage, peaksDataset
plotImage，peaksDataset
举例----------Examples----------
require(gcspikelite)
# paths and files[路径和文件]
gcmsPath<-paste(.find.package("gcspikelite"),"data",sep="/")
cdfFiles<-dir(gcmsPath,"CDF",full=TRUE)
eluFiles<-dir(gcmsPath,"ELU",full=TRUE)
# read data[读取数据]
pd<-peaksDataset(cdfFiles[1:3],mz=seq(50,550),rtrange=c(7.5,8.5))
# image plot[图像图]
plot(pd,rtrange=c(7.5,8.5),plotPeaks=TRUE,plotPeakLabels=TRUE)
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。
|
发表于 2012-2-25 17:36:52
