dba.plotBox(DiffBind)
dba.plotBox()所属R语言包：DiffBind
Boxplots
盒状图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Boxplots for read count distributions within differentially bound sites
盒形为内读取差异势必网站的数量分布
用法----------Usage----------
dba.plotBox(DBA, contrast=1, method=DBA$config$AnalysisMethod,
th=0.1, bUsePval=FALSE, bNormalized=TRUE,
attribute=DBA_GROUP,
bAll=FALSE, bAllIncreased=FALSE, bAllDecreased=FALSE,
bDB=TRUE, bDBIncreased=TRUE, bDBDecreased=TRUE,
pvalMethod=wilcox.test, bReversePos=FALSE, attribOrder,
vColors, varwidth=TRUE, notch=TRUE, ...)
参数----------Arguments----------
参数：DBA
DBA object.
DBA的对象。
参数：contrast
number of contrast to use for boxplot.
对比使用的盒形图。
参数：method
method used for analysis (used in conjunction with contrast):
用于分析（对比结合使用）的方法：
DBA_EDGER
DBA_EDGER
DBA_DESEQ
DBA_DESEQ
DBA_EDGER_BLOCK
DBA_EDGER_BLOCK
参数：th
significance threshold; all sites with FDR (or p-values, see bUsePval) less than or equal to this value will be included in the boxplot.
意义的阈值;与FDR的所有网站（或p值，见bUsePval）小于或等于这个值将被包括在盒形图。
参数：bUsePval
logical indicating whether to use FDR (FALSE) or p-value (TRUE) for thresholding.
逻辑指示是否使用阈值FDR（FALSE）或P-值（true）。
参数：bNormalized
logical indicating that normalized data (using normalization factors computed by differential analysis method) should be plotted. FALSE uses raw count data.
逻辑表明，规范化的数据（使用差分析方法计算的标准化因素）应绘制。假使用原始计数数据。
参数：attribute
attribute to use for determining groups of samples. Default (DBA_GROUP) plots the two groups used in the contrast. Possible values:
属性用于确定样本组。默认（DBA_GROUP）图的对比在两个组。可能的值：
DBA_GROUP
DBA_GROUP
DBA_ID
DBA_ID
DBA_TISSUE
DBA_TISSUE
DBA_FACTOR
DBA_FACTOR
DBA_CONDITION
DBA_CONDITION
DBA_REPLICATE
DBA_REPLICATE
DBA_CONSENSUS
DBA_CONSENSUS
DBA_CALLER
DBA_CALLER
DBA_CONTROL
DBA_CONTROL
参数：bAll
logical indicating if plot should include a set of boxplots using all counts, regardless of whether or not they pass the significance threshold.
逻辑表示如果图应包括一套使用所有计数的盒状图，不管他们是否传递意义的阈值。
参数：bAllIncreased
logical indicating if plot should include a set of boxplots using all counts that increase in affinity, regardless of whether or not they pass the significance threshold.
逻辑表明，如果图应包括一套使用所有计数的盒状图，增加亲和力，不管他们是否传递的意义阈值。
参数：bAllDecreased
logical indicating if plot should include a set of boxplots using all counts that decrease in affinity, regardless of whether or not they pass the significance threshold.
减少的亲和力，无论通过与否，他们的意义阈值逻辑表明，如果图应包括一套使用所有计数的盒状图。
参数：bDB
logical indicating if plot should include a set of boxplots using all counts in significantly differentially bound sites (i.e. those that pass the significance threshold), regardless of whether they increase or decrease in affinity.
逻辑表明，如果图应包括一套使用所有罪状显著差异必然的网站（即那些通过的意义阈值）的盒状图，不管他们是否增加或减少亲和力。
参数：bDBIncreased
logical indicating if plot should include a set of boxplots using all counts in significantly differentially bound sites that increase in affinity.
逻辑表明，如果图应包括在网站显著差异必然在亲和力增加了一套使用所有计数的盒状图。
参数：bDBDecreased
logical indicating if plot should include a set of boxplots using all counts in significantly differentially bound sites that decrease in affinity.
逻辑表明，如果图应包括一套使用所有计数的盒状图，在网站的显著差异必然在亲和力下降。
参数：pvalMethod
method to use when computing matrix of p-values. If NULL, no matrix is computed, and NULL is returned; this may speed up processing if there are many boxplots.
计算p值矩阵时使用的方法。如果为NULL，没有矩阵计算，则返回NULL，这可能会加快处理速度，如果有很多的盒状图。
参数：bReversePos
logical indicating if the default definition of positive affinity (higher affinity in the second group of the contrast) should be reversed (i.e. positive affinity is defined as being higher in the first group of the contrast).
逻辑说明，如果积极的亲和力（较高的亲和力，在第二组对比）的默认定义应扭转（即积极的亲和力定义为第一组高对比度）。
参数：attribOrder
vector of group numbers used to change the order that groups are plotted. If NULL, default order is used (group order for DBA_GROUP, and the order the attribute values appear for other values of attribute).
向量组用来改变组绘制的顺序号码。如果为NULL，默认的顺序是（组顺序为DBA_GROUP，和其他属性值的属性值中出现的顺序）。
参数：vColors
vector of custom colors; if absent, default colors will be used.
自定义颜色的向量;如果缺席，将使用默认的颜色。
参数：varwidth
passed to boxplot
传递到盒形图
参数：notch
passed to boxplot
传递到盒形图
参数：...
other arguments passed to boxplot
其他参数传递到盒形图
Details
详情----------Details----------
Draws a boxplot showing distributions of read counts for various groups of samples under various conditions. In default mode, draws six boxes: one pair of boxes showing the distribution of read counts within all significantly differentially bound sites (one box for each sample group), one pair of boxes showing the distribution of read counts for significantly differentially bound sites that increase affinity in the second group, and a second pair of boxes showing the distribution of read counts for significantly differentially bound sites that have higher mean affinity in the first group.
绘制盒形图显示读取计数各组样品在不同条件下的分布。在默认模式下，提请6盒：一对阅读数分布均显着差异必然的网站为每个样本组（一箱）内，一对的读取计数分布显示盒盒显著差异必然的网站，增加在第二组，第二双盒的读取计数的分布呈现出显著差异必然在第一组中有较高的平均亲和力的网站的亲和力。
值----------Value----------
if pvalMethod is not NULL, returns a matrix of p-values indicating the significance of the difference between each pair of distributions.
如果pvalMethod不为NULL，返回一个表示对彼此之间的分布差异的意义p值的矩阵。
作者（S）----------Author(s)----------
Rory Stark
举例----------Examples----------
data(tamoxifen_analysis)
#default boxplot includes all DB sites, then divided into those increasing [默认的盒形图，包括所有DB的网站，然后进入越来越多的划分]
# affinity in each group[在每个组的亲和力]
dba.plotBox(tamoxifen)
# plot non-normalized data for DB sites by tissue[图非规范化的数据组织的DB网站]
# (changing order to place Resistant samples last)[（改变为了将最后抗样本）]
dba.plotBox(tamoxifen, attribute=DBA_TISSUE, bDBIncreased=FALSE,
bDBDecreased=FALSE, attribOrder=c(2,3,5,1,4), bNormalized=FALSE)
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 16:39:36
