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

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classify(flowPhyto)
classify()所属R语言包：flowPhyto

                                        Cluster the different Phytoplankton Populations
                                         聚类中的不同的浮游植物

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Classify the different cell populations from an OPP or FCS dataframe according to a  pre-defined parameters of population definition
从OPP或FCS dataframe的不同的单元群分类，根据人口的定义预定义的参数

Because the characteristics of each phytoplankton populations varied according to environmental conditions and instrument settings, a customizable table of pre-defined parameters (pop.def) is used to help in gating the different phytoplankton populations.  The rows of the pop.def table represent the names of the different populations. The columns of the pop.def table represent the parameters used for gating and clustering the different populations. The function uses these pre-defined parameters and inputs a single OPP or FCS file to cluster cell populations using either flowClust or flowMeans package
因为每个浮游植物种群特征变化，根据环境条件和仪器设置，预定义的参数定制表（pop.def）用于门，以帮助不同的浮游植物种群。行的pop.def表代表不同人群的名称。的pop.def表列代表的门所使用的参数和聚类的不同人群。该函数使用这些预定义的参数，并输入一个单一的OPP或FCS文件聚类的单元群使用使用flowClust或flowMeans包


用法----------Usage----------


classify(x, pop.def=POP.DEF, func=2, varnames = CHANNEL.CLMNS.SM, numc=0, noise=0,  plot.cluster=FALSE, plot.assignment=FALSE, try.context='local',...)



参数----------Arguments----------

参数：x
an OPP or FCS dataframe.
OPP或FCS dataframe。


参数：pop.def
pop.def table that defines how to gate & cluster the events into populations.
pop.def表定义如何闸门及聚类成群体事件。


参数：func
Choose the clustering method, either flowClust (func = 1) or flowMeans (func = 2, by default) function
聚类分析方法的选择，要么flowClust（FUNC = 1）或flowMeans（FUNC = 2，默认情况下）功能


参数：varnames
A character vector specifying the variables (columns) to be included in clustering when choosing flowMeans.
指定一个字符向量聚类包括在选择flowMeans时必须在变量（列）。


参数：numc
Number of clusters when choosing flowMeans. If set to 0 (default) the value matches the number of populations defined in pop.def table . If set to NA, the optimal number of clusters will be estimated automatically.
的聚类在选择flowMeans时数。如果设置为0（默认）值pop.def表中定义的人口数量相匹配。如果设置为NA，最优簇数目将自动估计。


参数：noise
Set up the noise threshold for phytoplankton cells. Only cells with chlorophyll value higher than the noise will be clustered
成立浮游植物单元的噪声阈值。叶绿素值较高的噪声只有单元将聚集


参数：plot.cluster
Plot the output of clustering when choosing flowMeans
画出聚类输出时，选择flowMeans


参数：plot.assignment
Plot the output of Matching cluster number with cell population defined in pop.def.tab when choosing flowMeans
在选择flowMeans绘制输出匹配在pop.def.tab定义的单元群簇号


参数：try.context
Default value set up to 'local'
成立当地的默认值“


参数：...
additional arguments to be passed to the plot function
额外的参数被传递到绘图功能


值----------Value----------

an OPP or FCS dataframe like the input x but with an additional column 'pop' indicating population assignment
如输入x，但有一个额外的列流行人口分配OPP或FCS dataframe


举例----------Examples----------



## reading a standard SeaFlow file[＃阅读标准SeaFlow文件，]
opp.path <- system.file("extdata","seaflow_cruise","2011_001", "1.evt.opp",
                                package="flowPhyto")
pop.def.path <- system.file("extdata","seaflow_cruise","pop.def.tab",
                                package="flowPhyto")

opp <- readSeaflow(opp.path)
def <- readPopDef(pop.def.path)
pop <- classify(x=opp, pop.def= def)

table(pop$pop)

## reading from a fcs file format[＃从FCS文件格式阅读]
fcs.file.path <- system.file("extdata","fcs_cruise", "CD.20070615.A.0010.fcs",
                                package="flowPhyto")
pop.def.path2 <- system.file("extdata","fcs_cruise", "pop.def.tab",
                                package="flowPhyto")

require(flowClust)
ff <- read.FCS(fcs.file.path, transformation=FALSE)
df <- caroline::tab2df(exprs(ff))
names(df) <- EVT.HEADER[c(2,6,5,8,7,NA,9,NA,NA,10,1)]

#if(!all(EVT.HEADER[5:length(EVT.HEADER)] %in% names(df)))[如果（（EVT.HEADER [5：长度（EVT.HEADER）]％％名（DF）））]
#  warning('Match your column names to the EVENT.COLUMN.NAMES')[警告（“匹配列名的EVENT.COLUMN.NAMES）]
def2 <- readPopDef(pop.def.path2)
pop2 <- classify(x=df, pop.def= def2, func=1)

table(pop2$pop)

#plotCytogram(pop2, 'fsc_small', 'chl_small', pop.def=def2)[plotCytogram（POP2，fsc_small，chl_small“，pop.def = def2）]

#optionally write this exported dataframe to disk as an opp file  [可选写这个出口dataframe作为OPP文件到磁盘]
#writeSeaflow('converted.fcs.evt', df)[writeSeaflow（converted.fcs.evt，DF）]


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


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