R语言 idiogram包 idiogram()函数中文帮助文档(中英文对照)

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idiogram(idiogram)
idiogram()所属R语言包：idiogram

                                         Plotting of Genomic Data
                                         绘制的基因组数据

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Function for plotting genomic data along with corresponding cytogenetic banding information
绘制基因组数据，以及相应的单元遗传学带信息的功能


用法----------Usage----------


idiogram(data, genome, chr=NULL, organism=NULL,
method=c("plot","matplot","image"), margin=c("ticks","idiogram"),
grid.col=c("red","grey"), grid.lty=c(1,2), widths=c(1,2),
relative=FALSE, dlim=NULL, main=NA, xlab=NA,
ylab=NA,cex.axis=.7,na.color = par("bg"),cen.color="red", mb=FALSE,
...)



参数----------Arguments----------

参数：data
a vector or matrix of numeric data to plot. The names/rownames attribute needs to contain corresponding gene identifiers
一个向量或矩阵的积数值数据。名/ rownames属性需要包含相应的基因标识


参数：genome
a chromLocation object associated with the specified data set. See below for details.  
1 chromLocation对象与指定的数据集。细节见下文。


参数：chr
which chromosome to plot  
染色体绘制


参数：organism
if NULL, determination of the host organism will be retrieved from the organism slot of the chromLocation object. Otherwise "h", "r", or "m" can be used to specify human, rat, or mouse chromosome information
如果为NULL，宿主生物体的决心，将取自organism的chromLocation对象插槽。否则"h"，"r"或"m"可以用来指定人类，大鼠，小鼠染色体信息


参数：method
plotting method  
绘制方法


参数：margin
type of banding information to display in the plot margin
带信息显示在小区边缘的类型


参数：grid.col
a two element vector specifying the centromere and band grid colors.
两个元素的向量指定的着丝粒和带网格的颜色。


参数：grid.lty
a two element vector specifying the centromere and band grid line type.
两个元素的向量指定的着丝粒和带网格线类型。


参数：widths
a two element vector specifying the relative width of the margin idiogram two the adjacent graph. This option is currently ignored.
两个元素的向量指定的保证金idiogram两个相邻的图的相对宽度。目前正在忽略此选项。


参数：relative
If relative is TRUE, the vertical height of the plot is scaled relative to the size of largest chromosome.
relative如果为TRUE，该图的垂直高度是相对缩小规模最大的染色体。


参数：dlim
a two element vector specifying the minimum and maximum values for x.  Data in x that exceed the min and max limits will be set to the min/max limit values before plotting.
两个元素的向量指定为x最低和最高值。数据x超过图将之前设置的最小和最大限制到最小/最大限值。


参数：main
an overall title for the plot. Defaults to the chromosome name.
图的总冠军。染色体的默认名称。


参数：xlab
a title for the x axis.
X轴的标题。


参数：ylab
a title for the y axis.
为Y轴的标题。


参数：cex.axis
the magnification to be used for axis annotation relative to the current.
用于轴标注相对于当前的放大倍率。


参数：na.color
color to be used for NA values, defaults to: par("bg")
颜色为无值，默认为：面值（“BG”）


参数：cen.color
color to be used for the centromere when margin="idiogram", defaults to: "red"   
着丝粒的保证金=“idiogram”，默认时使用的颜色：“红色”


参数：mb
if TRUE, subset data to include just those row names starting with the value of the argument chr. Otherwise, use chromLoc as outlined below.
如果TRUE，data只包含那些行名称与参数chr值的子集。否则，使用chromLoc概述如下。


参数：...
additional graphical parameters can be given as arguments.
额外的图形参数可以作为参数。


Details

详情----------Details----------

This function displays cytogenetic banding information in the plot margin and calls a secondary plotting function to display associated data at the same relative position.  Cytogenetic data for human, mouse, and rat genomes are currently included.
此功能显示在小区边缘的单元遗传学信息带，并调用一个辅助绘图功能，在相同的相对位置的相关数据显示。目前包含人类，小鼠和大鼠的基因组，单元遗传学数据。

The data is arranged by associating gene identifiers to genomic location using a chromLoc annotation object built using the buildChromLocation function from the annotation package. As such, a vector of data is to be plotted, the names attribute of the vector needs to contain the gene identifiers.  Likewise if a matrix of data is to be plotted, the rownames attribute of the matrix needs to contain the gene identifiers.
数据关联基因标识基因的位置，使用安排chromLoc使用buildChromLocation的函数注释包注释对象。正因为如此，一个数据的向量，是要绘制，names属性的向量，需要包含的基因标识。同样，如果要绘制的数据矩阵，rownames矩阵的属性必须包含的基因标识。

To date, plot can be called for vector data, while matplot and image can be called for matrix data.  Most additional plotting arguments can be passed down via ....  However, the idiogram function plots the axis independently. Currently, only the cex.axis,col.axis, and font.axis parameters are intercepted from ... and redirected to the specialized axis call. Other parameters that effect the axis should be set via par.
迄今为止，plot可以称为矢量数据，而matplot和image可以称为矩阵数据。大多数额外的绘图参数可以通过下通过......然而，idiogram功能绘制轴独立。目前，只有cex.axis，col.axis，font.axis参数截获...重定向到专门axis呼叫。其他参数，效果轴应通过par。

The function midiogram is a simple wrapper around idiogram to plot all the chromosomes from a particular organism using sensible default values. The "m" refers to plotting multiple idiograms.
功能midiogram是围绕idiogram简单的包装来绘制所有的染色体从一个特定的有机体，使用合理的默认值。 "m"是指绘制多个idiograms。


作者（S）----------Author(s)----------


Kyle Furge <kyle.furge@vai.org> and Karl Dykema
<karl.dykema@vai.org>



参见----------See Also----------

buildChromLocation,
buildChromLocation


举例----------Examples----------


library(idiogram)

## [＃]
## NOTE:This requires an annotation package to work.[＃注：这需要一个注解包工作。]
##      In this example packages "hu6800.db" and "golubEsets" are used.[＃在这个例子中包“hu6800.db”和“golubEsets”使用。]
##      They can be downloaded from http://www.bioconductor.org[＃他们可以从http://www.bioconductor.org下载]
##      "hu6800.db" is under MetaData, "golubEsets" is under Experimental[＃“hu6800.db”是根据元数据，“golubEsets”下的实验]
##      Data.[＃数据。]


if(require(hu6800.db) && require(golubEsets)) {
   library(golubEsets)
   data(Golub_Train)

   hu.chr <- buildChromLocation("hu6800")
   ex <- assayData(Golub_Train)$exprs[,1]

   ## make sure the names() attribute is set correctly[＃确保名称（）属性设置正确]
   gN <- names(ex)
   gN[1:10]   

   idiogram(ex,hu.chr,chr="1")

   colors <- rep("black",times=length(ex))
   colors[ex > 10000] <- "red"
   pts <- rep(1,times=length(ex))
   pts[ex > 10000] <- 2
   idiogram(ex,hu.chr,chr="1",col=colors,pch=pts,font.axis=2,cex.axis=1)
   abline(v=0,col="darkgreen")

   ## An example of the dlim option. It is most useful for making[＃例如的dlim选项。它是制作最有用]
   ## consistant multi-panel plots[＃洽场的多面板图]
   colors <- rep("black",times=length(ex))
   colors[ex > 10000] <- "red"
   colors[ex < 0] <- "blue"

   idiogram(ex,hu.chr,chr="1",col=colors,xlim=c(-3000,21000))
   idiogram(ex,hu.chr,chr="1",col=colors,dlim=c(-100,7500),xlim=c(-3000,21000))
   idiogram(ex,hu.chr,chr="1",col=colors,dlim=c(-100,7500),xlim=c(-3000,10000))

   ## Using the identify function[＃使用识别功能]
   ip <- idiogram(ex,hu.chr,chr="1",col=colors,pch=19)
   #identify(ip$x,ip$y,labels=ip$labels)[标识（IP $ X，IP $ Y，标签= IP $标签）]
   
} else print("This example requires the hu6800.db and golubEsets data packages.")

## The example data is BAC array CGH data from J. Fridlyand's[＃示例数据是BAC的阵列CGH数据从研究Fridlyand的]
## aCGH package[＃aCGH包]

data(idiogramExample)

idiogram(colo.eset[,1],ucsf.chr,chr="1")

idiogram(colo.eset,ucsf.chr,chr="1",method="image")

idiogram(colo.eset,ucsf.chr,chr="1",method="image",col=topo.colors(50),grid.lty=c(1,NA))

idiogram(colo.eset,ucsf.chr,chr="1",method="mat",type="l")

## for a consistant multi-panel plot it can be helpful to force the data[＃为洽场的多面板的图，它可以帮助迫使数据]
## range within each panel to a defined range using 'dlim'[＃每个小组范围内定义的范围，使用“dlim]
## This is similar to calling the 'midiogram' function[＃这是调用“midiogram”功能类似]

op <- par(no.readonly=TRUE)
par(mai=par("mai")*c(0.1,0.5,0.5,0.5))
layout(rbind(c(1:8),c(0,9:14,0),c(15:22)))

for(i in c(1:22)) {
  idiogram(colo.eset,ucsf.chr,chr=i,method="i",dlim=c(-1,1),margin="i",relative=TRUE)
}

par(op)

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


注：
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