plotEigengeneNetworks(WGCNA)
plotEigengeneNetworks()所属R语言包：WGCNA
Eigengene network plot
Eigengene网络图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function plots dendrogram and eigengene representations of (consensus) eigengenes networks. In the case of conensus eigengene networks the function also plots pairwise preservation measures between consensus networks in different sets.
此函数曲线聚类分析和eigengene的陈述（共识）的特征基因网络。在的情况下conensus eigengene网络的功能也图在不同的组两两之间的共识，网络保全措施。
用法----------Usage----------
plotEigengeneNetworks(
multiME,
setLabels,
letterSubPlots = FALSE, Letters = NULL,
excludeGrey = TRUE, greyLabel = "grey",
plotDendrograms = TRUE, plotHeatmaps = TRUE,
setMargins = TRUE, marDendro = NULL, marHeatmap = NULL,
colorLabels = TRUE, signed = TRUE,
heatmapColors = NULL,
plotAdjacency = TRUE,
printAdjacency = FALSE, cex.adjacency = 0.9,
coloredBarplot = TRUE, barplotMeans = TRUE, barplotErrors = FALSE,
plotPreservation = "standard",
zlimPreservation = c(0, 1),
printPreservation = FALSE, cex.preservation = 0.9,
...)
参数----------Arguments----------
参数：multiME
either a single data frame containing the module eigengenes, or module eigengenes in the multi-set format (see checkSets). The multi-set format is a vector of lists, one per set. Each set must contain a component data whose rows correspond to samples and columns to eigengenes.
无论是单个数据框包含模块的特征基因，或模块的特征基因的，在多组的格式（见checkSets）。多设置的格式是一个向量的列表，每一个组。每一组必须包含一个组成部分data的行对应的样品和列的特征基因。
参数：setLabels
A vector of character strings that label sets in multiME.
一个字符串向量，标签设置在multiME。
参数：letterSubPlots
logical: should subplots be lettered?
逻辑：应次要图字母？
参数：Letters
optional specification of a sequence of letters for lettering. Defaults to "ABCD"...
可选的刻字字母顺序的规格。默认为“ABCD”...
参数：excludeGrey
logical: should the grey module eigengene be excluded from the plots?
逻辑：应被排除在图灰色模块eigengene的？
参数：greyLabel
label for the grey module. Usually either "grey" or the number 0.
标签的灰色模块。通常要么是“灰色”或数字0。
参数：plotDendrograms
logical: should eigengene dendrograms be plotted?
逻辑：应eigengene树状图绘制？
参数：plotHeatmaps
logical: should eigengene network heatmaps be plotted?
逻辑：应eigengene网络热图绘制？
参数：setMargins
logical: should margins be set? See par.
逻辑：要利润？见par。
参数：marDendro
a vector of length 4 giving the margin setting for dendrogram plots. See par. If setMargins is TRUE and marDendro is not given, the function will provide reasonable default values.
一个向量的长度为4的页边距设置为树状图图。见par。如果setMargins是TRUE和marDendro不给，该功能将提供合理的默认值。
参数：marHeatmap
a vector of length 4 giving the margin setting for heatmap plots. See par. If setMargins is TRUE and marDendro is not given, the function will provide reasonable default values.
HeatMap在图的页边距设置为一个向量的长度为4。见par。如果setMargins是TRUE和marDendro不给，该功能将提供合理的默认值。
参数：colorLabels
logical: should module eigengene names be interpreted as color names and the colors used to label heatmap plots and barplots?
逻辑模块eigengene名被理解为颜色的名称和所使用的颜色标记的热图图和barplots的？
参数：signed
logical: should eigengene networks be constructed as signed?
逻辑：应eigengene网络构造签署？
参数：heatmapColors
color palette for heatmaps. Defaults to heat.colors when signed is FALSE, and to redWhiteGreen when signed is TRUE.
热图的调色板。默认为heat.colorssigned是FALSE，并redWhiteGreensigned是TRUE，。
参数：plotAdjacency
logical: should module eigengene heatmaps plot adjacency (ranging from 0 to 1), or correlation (ranging from -1 to 1)?
逻辑模块eigengene的热图图邻接（从0到1），或相关范围从-1到1？
参数：printAdjacency
logical: should the numerical values be printed into the adjacency or correlation heatmap?
逻辑的数值打印到相邻或相关热图？
参数：cex.adjacency
character expansion factor for printing of numerical values into the adjacency or correlation heatmap
字符膨胀系数的数值打印到相邻或相关热图
参数：coloredBarplot
logical: should the barplot of eigengene adjacency preservation distinguish individual contributions by color? This is possible only if colorLabels is TRUE and module eigengene names encode valid colors.
的barplot eigengene邻接保存逻辑：应区分个人贡献的颜色？这是可能的，只有colorLabels是TRUE和的模块eigengene名有效颜色进行编码。
参数：barplotMeans
logical: plot mean preservation in the barplot? This option effectively rescales the preservation by the number of eigengenes in the network. If means are plotted, the barplot is not colored.
逻辑：图平均保存在barplot，？这个选项有效地保护网络中的特征基因的数量重新调整。如果绘制方式，barplot不着色。
参数：barplotErrors
logical: should standard errors of the mean preservation be plotted?
逻辑：应绘制标准误差的平均保存？
参数：plotPreservation
a character string specifying which type of preservation measure to plot. Allowed values are (unique abbreviations of) "standard", "hyperbolic", "both".
一个字符串，指定绘制哪种类型的保全措施。允许的值是（）"standard"，"hyperbolic"，"both"唯一的缩写。
参数：zlimPreservation
a vector of length 2 giving the value limits for the preservation heatmaps.
一个向量长度为2的值限制保护热图。
参数：printPreservation
logical: should preservation values be printed within the heatmap?
逻辑：应保存价值的印在热图？
参数：cex.preservation
character expansion factor for preservation display.
保存显示的字符膨胀系数。
参数：...
other graphical arguments to function labeledHeatmap.
其他图形参数传递给函数labeledHeatmap。
Details
详细信息----------Details----------
Consensus eigengene networks consist of a fixed set of eigengenes "expressed" in several different sets. Network connection strengths are given by eigengene correlations. This function aims to visualize the networks as well as their similarities and differences across sets.
共识的eigengene网络由一组固定“表示”在几个不同的特征基因。网络连接的优势eigengene的相关性。此功能的目的是可视化的网络以及整个组的相似性和差异。
The function partitions the screen appropriately and plots eigengene dendrograms in the top row, then a square matrix of plots: heatmap plots of eigengene networks in each set on the diagonal, heatmap plots of pairwise preservation networks below the diagonal, and barplots of aggregate network preservation of individual eigengenes above the diagonal. A preservation plot or barplot in the row i and column j of the square matrix represents the preservation between sets i and j.
的功能分区适当屏幕和图eigengene聚类在顶行中，然后图：每个集合中的对角线上的，热图图对角线以下的成对保存网络的热图图eigengene网络的正方形矩阵，和总的网络保存barplots对角线以上的个别特征基因。一个保存的图或barplot在该行i和第j列的方阵代表的保护套i和j之间的。
Individual eigengenes are labeled by their name in the dendrograms; in the heatmaps and barplots they can optionally be labeled by color squares. For compatibility with other functions, the color labels are encoded in the eigengene names by prefixing the color with two letters, such as "MEturquoise".
个人特征基因标记，他们的名字在树状图，在热图和barplots的，他们可以选择的颜色方块标记。与其他功能的兼容性，色彩标签进行编码在eigengene名称的前缀有两个字母的颜色，如"MEturquoise"。
Two types of network preservation can be plotted: the "standard" is simply the difference between adjacencies in the two compared sets. The "hyperbolic" difference de-emphasizes the preservation of low adjacencies. When "both" is specified, standard preservation is plotted in the lower triangle and hyperbolic in the upper triangle of each preservation heatmap.
可以绘制两种类型的网络保护："standard"简直是相邻的两个比较组之间的差异。 "hyperbolic"差异强调保存低邻接。当"both"指定，绘制标准保存的下三角和双曲线保存热图上三角形的每个。
If the eigengenes are labeled by color, the bars in the barplot can be split into segments representing the contribution of each eigengene and labeled by the contribution. For example, a yellow segment in a bar labeled by a turquoise square represents the preservation of the adjacency between the yellow and turquoise eigengenes in the two networks compared by the barplot.
如果特征基因中被标记为通过颜色，被分割的条形在barplot可以代表每个eigengene的贡献成段，和标记的贡献。例如，一个黄色标记的绿松石广场的一间条形段的barplot相比在两个网络之间的黄色和绿松石特征基因的邻接保存。
For large numbers of eigengenes and/or sets, it may be difficult to get a meaningful plot fit a standard computer screen. In such cases we recommend using a device such as postscript or pdf where the user can specify large dimensions; such plots can be conveniently viewed in standard pdf or postscript viewers.
对于大量的特征基因和/或组，它可能很难得到一个有意义的图符合标准的计算机屏幕上。在这种情况下，我们建议使用的设备，如postscript或pdf，用户可以在指定的大尺寸，这样的图可以方便地查看标准的PDF或PostScript观众。
值----------Value----------
None.
无。
（作者）----------Author(s)----------
Peter Langfelder
参考文献----------References----------
modules. BMC Systems Biology 2007, 1:54
参见----------See Also----------
labeledHeatmap, labeledBarplot for annotated heatmaps and barplots;
labeledHeatmap，labeledBarplot为注释热图和barplots的;
hclust for hierarchical clustering and dendrogram plots
hclust层次聚类和聚类分析图
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 21:21:52
