resplot(GSEAlm)
resplot()所属R语言包：GSEAlm
Simple Graphical Summaries for Gene Set Enrichment Analysis
基因组富集分析简单的图形摘要
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Diagnostic plots for GSEA. 'resplot' and 'restrip' group residuals (or expression levels) from a specific gene-set by sample. 'mnDiffPlot' shows mean expression differences for a dichotomous phenotype, by gene, for a specific gene set.
GSEA诊断图。 “resplot”和“restrip组残差从特定的基因组由样品（或表达水平）。 “mnDiffPlot”节目，平均为二元型基因的表达差异，对于一个特定的基因组。
用法----------Usage----------
resplot(GSname = "All", resmat, incidence = dumminc(resmat), fac,
atomic = "Gene", core.text = "Residuals by Sample",
yname = "Standardized Residual", xname = "Sample ID",
ID = colnames(resmat), lims = 0, gnames = levels(factor(fac)),
prefix = "", horiz = FALSE, colour=5,pch='+',...)
restrip(GSname = "All", resmat, incidence = dumminc(resmat), fac,
atomic = "Gene", core.text = "Residuals by Sample",
yname = "Standardized Residual", xname = "Sample ID", ID = colnames(resmat),
gnames = levels(factor(fac)), prefix = "", colour=c(2:4,6), resort=TRUE,
horiz = FALSE, resort.fun=num.positive, pch='+', ...)
mnDiffPlot(GSname = "All", exprmat, incidence = dumminc(exprmat), fac,
atomic = "Gene", core.text = paste("Mean Expression Difference by",atomic),
yname="Log Expression Ratio", xname="Log Expression",
gnames = levels(factor(fac)), prefix = "", fitline=FALSE, varsize=FALSE,
参数----------Arguments----------
参数：GSname
Gene-set Name. See "Details".
基因组的名称。查看“详细信息”。
参数：resmat,exprmat
Numerical matrix with the values to be plotted. See "Details".
值的数值矩阵绘制。查看“详细信息”。
参数：incidence
Gene-set 0/1 membership matrix
基因组0/1隶属度矩阵
参数：fac
The phenotypical variable to plot by. Must be discrete. For 'mnDiffPlot', must be dichotomous.
绘制的表型变量。必须是独立的。为mnDiffPlot，必须是二分法。
参数：atomic
string identifying the meaning of rows in the data matrix. Defaults to "Gene".
字符串识别数据矩阵中的行的意义。默认为“基因”。
参数：core.text,gnames,prefix,xname,yname
strings controlling the text of main and axis captions
控制的主要和轴标题的文本字符串
参数：ID
Group names associated with the data matrix columns
组相关数据矩阵的列名
参数：lims
plotting limits for the response axis
为响应轴绘制的限制
参数：horiz
logical: whether the boxplots or strips should be horizontal (defaults to FALSE)
逻辑：盒形或条状是否应该水平（默认为false）
参数：colour
color of boxplot filling ('resplot') or symbols ('restrip')
颜色填充盒形图（resplot）或符号（restrip）
参数：pch
the plotting symbol
图形符号
参数：resort
('restrip' only) whether to sort groups for better visibility
（restrip只）有否更好的可视性组排序
参数：resort.fun
('restrip' only) what function to sort groups by. Ignored unless 'resort==TRUE'. See stripchart documentation for more details
（“restrip只）函数进行排序分组。被忽略，除非“度假== TRUE”。详情请参阅stripchart文件
参数：fitline
('mnDiffPlot' only) logical: whether a loess fit should be plotted
（“mnDiffPlot唯一的）逻辑：是否的FIT应绘制黄土
参数：varsize
('mnDiffPlot' only) logical: whether symbol sizes should be proportional to (t-test style) standard errors
（“mnDiffPlot）逻辑：符号大小是否应该成正比（t检验作风）标准误差
参数：reverse
('mnDiffPlot' only)logical: whether the factor's order should be reversed so that the second level is on the x-axis rather than the first one
（“mnDiffPlot）逻辑：使第二个层次是在x轴，而不是第一个因素的订单是否应扭转
参数：...
Additional graphical parameters passed on to the generic plotting functions.
额外的图形参数传递到通用的绘图功能。
Details
详情----------Details----------
These functions provide simple graphical summaries for processed gene-expression data, or other similar datasets for which matrix form is useful. They are tailored predominantly for GSEA, but are useful in general as well.
这些功能提供简单的图形摘要基因表达数据处理，或其他类似的数据集，是有用的矩阵形式。他们主要为GSEA量身定做，但一般也非常有用。
'resplot' calls boxplot and 'restrip' calls stripchart; both summarize *all* data points from those rows in 'resmat' which are members in the gene-set specified by 'GSname'. The summary is by column. For each level of 'fac' there will be a separate pane.
“resplot调用boxplot”restrip的来电stripchart;既总结所有数据点从在“resmat那些行，这是在基因组由”GSname指定成员。摘要列。对于每个因素的水平会有一个单独的窗格中。
'mnDiffPlot' calls plot; it plots the mean differences, by row, between columns belonging to the two groups specified by 'fac', as a function of the mean values for the first group alone. Each row translates to a single point on the graph. Again, the summary is only for rows indicated by 'GSname'.
“mnDiffPlot”呼叫plot;图的平均差异，按行，列属于“FAC”指定的两个组之间的功能仅在第一组的平均值。每一行转换为单点上的图形。再次，总结是只为GSname表示行。
For gene-set selective plots to properly work, the incidence matrix needs to have non-empty row names, and 'GSname' must match one of them.
关联矩阵为基因组选择性图的正常工作，需要有非空行名称，必须符合“GSname其中之一。
If both 'GSname' and 'incidence' are left blank, automatic utilities are called which help generate a summary of the entire matrix, by column.
如果都“GSname”和“发病率”都留空，被称为自动公用事业有助于产生整个矩阵的总结，由列。
All functions plot a reference line signalling zero. 'mnDiffPlot' also optionally plots a loess fit for expression differences (if 'fitline=TRUE').
所有的功能，绘制参考线，信号为零。 “mnDiffPlot也可选择图为差异表达的黄土适合（如果fitline = TRUE”）。
注意----------Note----------
One can use 'resplot'/'restrip' to plot raw expression values rather than residuals; it all depends on what's in the data matrix.
一个可以使用“resplot/restrip绘制原始表达式的值，而不是残差，这一切取决于对数据矩阵是什么。
作者（S）----------Author(s)----------
Assaf Oron
参见----------See Also----------
boxplot,plot,stripchart,par,GOmnplot
boxplot，plot，stripchart，par，GOmnplot
举例----------Examples----------
data(sample.ExpressionSet)
lm1 = lmPerGene(sample.ExpressionSet,~sex)
r1 = getResidPerGene(lm1)
### now a boxplot of all residuals by sample[＃＃现在所有残差由样品的盒形图]
resplot(resmat=exprs(r1),fac=sample.ExpressionSet$sex)
### This plot is not very informative because of some gross outliers;[＃＃这个图是不会因为一些毛离群非常翔实;]
### try this instead[＃尝试这种替代]
resplot(resmat=exprs(r1),fac=sample.ExpressionSet$sex,lims=c(-5,5))
### stripchart for first 10 genes[＃第10个基因stripchart]
restrip(resmat=exprs(r1)[1:10,],fac=sample.ExpressionSet$type,prefix="Not")
### note the wild trajectory of the loess fit:[＃注意的黄土适合野生轨迹：]
mnDiffPlot(exprmat=exprs(sample.ExpressionSet),fac=sample.ExpressionSet$type,xname="Raw Expression",yname="Expression Difference",fitline=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。
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发表于 2012-2-25 21:18:31
