pChromPlot(ADaCGH2)
pChromPlot()所属R语言包：ADaCGH2
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Produce PNG figures of egment plots (by chromosome) for aCGH segmentation results. Internal calls are parallelized for increased speed and we use ff objets to allow the handling of very large objects. The output
产生的egment图aCGH分割结果（染色体）的PNG数字。内部通话并行增加的速度，我们使用FF艺术品允许处理非常大的对象。输出
用法----------Usage----------
pChromPlot(outRDataName, cghRDataName, chromRDataName,
probenamesRDataName,
posRDataName = NULL,
imgheight = 500,
pixels.point = 3,
pch = 20,
colors = c("orange", "red", "green", "blue", "black"),
imagemap = FALSE,
...)
参数----------Arguments----------
参数：outRDataName
The Rdata file name that contains the ffdf with the results from the segmentation as carried out by any of the pSegment functions.
的的RDATA文件名称包含的ffdf任何pSegment功能进行分割结果。
参数：cghRDataName
The Rdata file name that contains the ffdf with the aCGH data. This file can be created using as.ffdf with a data frame with genes (probes) in rows and subjects or arrays in columns. Function inputDataToADaCGHData produces these type of files.
RDATA文件名中包含的aCGH数据的ffdf。这个文件可以使用as.ffdf科目或行和列的阵列（探针）与基因数据框。功能inputDataToADaCGHData产生这些类型的文件。
参数：chromRDataName
The RData file name with the ff (short integer) vector with the chromosome indicator. Function inputDataToADaCGHData produces these type of files.
与FF（短整数）与染色体指标向量的RDATA文件名称。功能inputDataToADaCGHData产生这些类型的文件。
参数：probenamesRDataName
The RData file name with the vector with the probe names. Function inputDataToADaCGHData produces these type of files. Note that this is not an ff file.
探针名称向量的RDATA文件名称。功能inputDataToADaCGHData产生这些类型的文件。请注意，这不是一个FF文件。
参数：posRDataName
The RData file name with the ff double vector with the location (e.g., position in kbases) of each probe in the chromosome. Function inputDataToADaCGHData produces these type of files. Used for the spacing in the plots. If NULL, the x-axis goes from 1:number of probes in that chromosome.
与FF每个探针的位置，在染色体上（例如，位置在kbases）双向量的的RDATA文件名称。功能inputDataToADaCGHData产生这些类型的文件。用于图间距。如果为NULL，x轴是从1：探针，染色体的数目。
参数：imgheight
Height of png image. See png.
png图像的高度。看到png。
参数：pixels.point
Approximate number of pixels that each point takes; this determines also final figure size. With many probes per chromosome, you will want to make this a small value.
像素，每个点需要的大致数量;这也决定了最后的数字大小。与每个染色体的许多探针，你会想这是一个较小的值。
参数：pch
The type of plotting symbol. See par.
绘制符号的类型。看到par。
参数：colors
A five-element character vector with the colors for: probes without change, probes that have a "gained" status, probes that have a "lost" status, the line that connects (smoothed values of) probes, the horizontal line at the 0 level.
五行与颜色特征向量：没有改变，有一个“虎子”的地位，有“失落”的状态，线路连接探针（平滑值），水平线的探针的探针，探针0级。
参数：imagemap
If FALSE only the png figure is produced. If TRUE, for each array * chromosome, to additional files are produced: "pngCoord_ChrNN@MM" and "geneNames_ChrNN@MM", where "NN" is the chromosome number and "MM" is the array name. The first file contains the coordinates of the png and radius and the second the gene or probe names, so that you can easily produce an HTML imagemap. (Former versions of ADaCGH did this automatically with Python. In this version we include the Python files under "imagemap-example".)
如果为FALSE，只有PNG图制作。如果是TRUE，每个数组*染色体，其他文件是：“pngCoord_ChrNN @ MM的”和“geneNames_ChrNN @ mm”，“NN”是染色体数目的“MM”是数组名。第一个文件包含PNG和半径的坐标和第二个基因或探针名称，这样你可以很容易地产生一个HTML的imagemap。 （以前版本的ADaCGH这样做自动与Python。在这个版本中，我们包括下“的imagemap例如”Python文件。）
参数：...
Additional arguments; not used.
额外的参数，不使用。
值----------Value----------
Used only for its side effects of producing PNG plots, stored in the current working directory (getwd().)
仅用于它的副作用产生的PNG图存储在当前工作目录（getwd()。）
作者（S）----------Author(s)----------
Ramon Diaz-Uriarte <a href="mailto:rdiaz02@gmail.com">rdiaz02@gmail.com</a>
参见----------See Also----------
pSegment
pSegment
举例----------Examples----------
## Create a temp dir for storing output[＃创建一个临时目录，用于存储输出。]
dir.create("ADaCGH2_plot_tmp_dir")
originalDir <- getwd()
setwd("ADaCGH2_plot_tmp_dir")
## Start cluster[＃启动聚类]
snowfallInit(universeSize = 2, typecluster = "SOCK")
## To speed up R CMD check, we do not use inputEx1, but a much smaller[＃为了加快R CMD检查，我们不使用inputEx1，但要小得多]
## data set. When you try the examples, you might one to use[＃设置数据。当您尝试的例子，你可能要使用的]
## inputEx1 instead.[＃inputEx1代替。]
## Not run: [＃无法运行：]
fname <- list.files(path = system.file("data", package = "ADaCGH2"),
full.names = TRUE, pattern = "inputEx1")
## End(Not run)[＃结束（不运行）]
fname <- list.files(path = system.file("data", package = "ADaCGH2"),
full.names = TRUE, pattern = "inputEx2")
tableChromArray <- inputDataToADaCGHData(filename = fname)
hs_mad.out <- pSegmentHaarSeg("cghData.RData",
"chromData.RData", merging = "MAD")
save(hs_mad.out, file = "hs_mad.out.RData", compress = FALSE)
pChromPlot(outRDataName = "hs_mad.out.RData",
cghRDataName = "cghData.RData",
chromRDataName = "chromData.RData",
posRDataName = "posData.RData",
probenamesRDataName = "probeNames.RData",
imgheight = 350)
## Not run: [＃无法运行：]
## Produce the coordinate and probe names files.[＃产生的坐标和探针名称的文件。]
pChromPlot(outRDataName = "hs_mad.out.RData",
cghRDataName = "cghData.RData",
chromRDataName = "chromData.RData",
posRDataName = "posData.RData",
probenamesRDataName = "probeNames.RData",
imgheight = 350,
imagemap = TRUE)
## End(Not run)[＃结束（不运行）]
### PNGs are in this directory[＃＃PNG图像在此目录]
getwd()
### Explicitly stop cluster[＃明确停止聚类]
sfStop()
### Clean up (DO NOT do this with objects you want to keep!!!)[＃清理（不跟你想保留的对象！！）]
load("chromData.RData")
load("posData.RData")
load("cghData.RData")
delete(cghData); rm(cghData)
delete(posData); rm(posData)
delete(chromData); rm(chromData)
unlink("chromData.RData")
unlink("posData.RData")
unlink("cghData.RData")
unlink("probeNames.RData")
lapply(hs_mad.out, delete)
rm(hs_mad.out)
unlink("hs_mad.out.RData")
### Try to prevent problems in R CMD check[＃尽量避免问题在R加利福尼亚检查]
Sys.sleep(2)
## To prevent CMD check from crashing after cleanEx[＃为了防止崩溃后cleanEx加利福尼亚检查]
detach("package:rlecuyer", unload = TRUE)
### Delete all png files and temp dir[＃删除所有PNG文件和temp目录]
setwd(originalDir)
Sys.sleep(2)
unlink("ADaCGH2_plot_tmp_dir", recursive = TRUE)
Sys.sleep(2)
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 11:03:35
