R语言 procoil包 plot-methods()函数中文帮助文档(中英文对照)

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plot-methods(procoil)
plot-methods()所属R语言包：procoil

                                        Plotting prediction profiles
                                         绘制预测概况

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Functions for plotting prediction profiles
预测剖面绘制功能


用法----------Usage----------


## S4 method for signature 'CCProfile,missing'
plot(x, col="red", rng=0,
             standardize=FALSE, shades=NULL,
             legend="", legend.pos="topright", ...)
## S4 method for signature 'CCProfile,CCProfile'
plot(x, y, col=c("red", "blue"), rng=0,
             standardize=FALSE, shades=NULL, legend=NULL,
             legend.pos="topright", ...)



参数----------Arguments----------

参数：x
Object of class CCProfile to be plotted with plot
对象类CCProfile绘制plot


参数：y
Object of class CCProfile to be plotted with plot (in case plot is called with two arguments to compare two profiles)
对象类CCProfileplot（plot的情况下用两个参数调用比较两个剖面绘制）


参数：col
Character string containing the name of the color in which the profile should be plotted (in case plot is called with one CCProfile argument). A vector of character strings containing the names of the two colors in which the profiles should be plotted (in case plot is called with two CCProfile arguments).
字符串包含在配置文件（plot一个CCProfile参数调用）应绘制的颜色名称。一个矢量字符字符串包含其中型材应绘制（plot两个CCProfile参数调用）的两个颜色的名称。


参数：rng
Argument that allows the user to preset the range of the profile plot. If 0 (default) or negative, the range is determined automatically from the values in the profile. Otherwise, the range is set to [-rng,rng].
论点，即允许用户预设剖面图的范围。如果0（默认）或负，范围是从配置文件中的值自动确定。否则，范围设置为[-rng,rng]。


参数：standardize
logical. If FALSE (default), the profile values si are displayed as they are with the value y=-b/L superimposed as a light gray line. If TRUE, the whole profile is shifted by -b/L and the light gray line is displayed at y=0.
逻辑。如果FALSE（默认），个人资料值si显示他们的价值y=-b/L作为一个浅灰色的线叠加。如果TRUE，整个轮廓被转移-b/L浅灰色线显示在y=0。


参数：shades
Vector of at least two color specifications (default: NULL). If not NULL, the background area above and below the base line  y=-b/L are shaded in colors shades[1] and shades[2], respectively.
至少有两个规格颜色的矢量（默认值：NULL）。如果不为NULL，基准线的上方和下方的背景区域y=-b/L是灰色的颜色shades[1]和shades[2]，分别。


参数：legend
A character string containing the legend/description of the profile (in case plot is called with one CCProfile argument). A vector of character strings containing the legends/descriptions of the profiles (in case plot is called with two CCProfile arguments). If empty, no legend is displayed.
一个字符串，其中包含的传说/配置文件的描述（在plot一个CCProfile参数调用）。一个字符字符串包含的传说/配置文件的说明（plot两个CCProfile参数调用）的向量。如果是空的，没有传说中显示出来。


参数：legend.pos
Position specification for legend (if legend is specified). Can either be a vector with coordinates or a single keyword like “topright” (see legend).
位置规范传说（如果legend指定）。可以是一个坐标或像“topright”单一关键字矢量（见legend）。


参数：...
all other arguments are passed to the standard plot command that is called internally to display the graphics window
所有其他参数传递给标准plot命令，被称为内部显示图形窗口


Details

详情----------Details----------

The plot function displays the profile as a step function over the sequence with the steps connected by vertical lines. The vertical plot range can be determined by the rng argument. The sequence and the heptad register are visualized below and above the profile, respectively. The value -b/L and the light gray line has the  following meaning: It is obvious that we can rewrite
plot函数与垂直线连接的步骤序列的步功能显示的个人资料。 rng参数可以由垂直的图范围。序列和七肽寄存器的可视化以下及以上的文件，分别为。值-b/L和浅灰色线具有以下含义：这是显而易见的，我们可以重写

as
如

so the discriminant function value f(x) can be understood as the sum of values (si(x) - (-b/L)), i.e. the area between the constant value  -b/L and the prediction profile. If the area above the light gray line is greater than the area below the light gray line, the sequence is predicted as trimer, otherwise as dimer.
所以判别函数值f(x)可以理解为值的总和(si(x) - (-b/L))，即区域之间的恒定值-b/L和预测剖面。如果上述区域的浅灰色线是大于浅灰色线以下区域，为三聚体预测序列，否则为二聚体。

If plot is called with two CCProfile arguments, the two profiles are plotted together to facilitate a comparison of profiles (e.g. wild type sequences versus mutants).
如果plot被称为两个CCProfile参数，这两个剖面绘制在一起比较方便的配置文件（如野生型序列与突变）。


值----------Value----------

Both variants of plot do not return any value.
两个变种plot不返回任何值。


作者（S）----------Author(s)----------


Ulrich Bodenhofer <a href="mailto:bodenhofer@bioinf.jku.at">bodenhofer@bioinf.jku.at</a>



参考文献----------References----------


Hochreiter, S. (2011) Complex networks govern coiled coil oligomerization - predicting and profiling by means of a machine learning approach. Mol. Cell. Proteomics.

参见----------See Also----------

procoil, CCModel,
procoil，CCModel


举例----------Examples----------


## predict oligomerization of GCN4 wildtype[＃预测因子GCN4野生齐聚]
GCN4wt<-predict(PrOCoilModel,
                "MKQLEDKVEELLSKNYHLENEVARLKKLV",
                "abcdefgabcdefgabcdefgabcdefga")

## plot profile[＃图轮廓]
plot(GCN4wt)

## predict oligomerization of a GCN4 mutant[＃预测齐聚一因子GCN4突变]
GCN4m3<-predict(PrOCoilModel,
                "MKQLEDKVEELLSKIYHNENEVARLKKLV",
                "abcdefgabcdefgabcdefgabcdefga")

## plot two profiles[＃绘制两个剖面]
plot(GCN4wt, GCN4m3, legend=c("GCN4 wild type", "GCN4 mutant"))

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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