densityplot(flowViz)
densityplot()所属R语言包：flowViz
One-dimensional density plots for flow data
流量数据的一维密度图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
For flowSets the idea is to horizontally stack plots of density estimates for all frames in the flowSet for one or several flow parameters. In the latter case, each parameter will be plotted in a separate panel, i.e., we implicitely condition on parameters.
flowSets的想法是水平堆叠在一个或多个流量参数的flowSet所有帧的密度估计图。在后一种情况下，每个参数将被绘制在一个单独的面板，也就是说，我们implicitely对参数条件下。
用法----------Usage----------
## method for 'flowSet' objects
## S4 method for signature 'formula,flowSet'
densityplot(
x,
data,
channels,
xlab,
as.table=TRUE,
overlap=0.3,
prepanel=prepanel.densityplot.flowset,
panel = panel.densityplot.flowset,
filter=NULL,
scales=list(y=list(draw=F)),
groups,
...)
## method for 'flowFrame' objects
## S4 method for signature 'formula,flowFrame'
densityplot(
x,
data,
...)
prepanel.densityplot.flowset(
x,
y,
darg=list(n=50, na.rm=TRUE),
frames,
overlap=0.3,
subscripts,
...,
which.channel)
panel.densityplot.flowset(
x,
y,
darg=list(n=50, na.rm=TRUE),
frames,
channel,
overlap = 0.3,
channel.name,
filter=NULL,
fill=superpose.polygon$col,
lty=superpose.polygon$lty,
lwd=superpose.polygon$lwd,
alpha=superpose.polygon$alpha,
col=superpose.polygon$border,
groups=NULL,
refline=NULL,
margin=0.005,
gpar,
...)
## methods for various workflow objects
## S4 method for signature 'formula,view'
densityplot(
x,
data,
...)
## S4 method for signature 'view,missing'
densityplot(
x,
data,
channels,
...)
参数----------Arguments----------
参数：x
A formula describing the structure of the plot and the variables to be used in the display. The structure of the formula is factor ~ parameter, where factor can be any of the phenotypic factors in the phenoData slot or an appropriate factor object and parameter is a flow parameter. Panels for multiple parameters are drawn if the formula structure is similar to factor ~ parameter1 + parameter2, and factor can be missing, in which case the sample names are used as y-variable. To facilitate programatic access, the formula can be of special structure factor ~ ., in which case the optional channel argument is considered for parameter selection. For the workflow methods, x can also be one of the several workflow objects.
公式描述的图和结构要在显示器中使用的变量。该公式的结构是factor ~ parameter，其中factorphenoData插槽中的表型的因素可以是任何的或适当的因素对象和parameter是一个流动的参数。绘制多个参数的面板，如果公式的结构是类似factor ~ parameter1 + parameter2，factor可缺少，在这种情况下，样品名称为y变量。为了便于程序化的访问，公式可以是特殊的结构factor ~ .，在这种情况下，可选的channel参数参数选择的考虑。对于工作流的方法，x也可以是几个工作流对象之一。
参数：data
A flow data object that serves as a source of data, either a flowFrame or flowSet, or one of the several workflow objects.
一个流的数据对象，作为一个数据源，无论是flowFrame或flowSet，或几个工作流对象之一。
参数：xlab
Label for data x axis, with suitable defaults taken from the formula
数据X轴的标签，采取合适的默认值从公式
参数：as.table, scales, darg
These arguments are passed unchanged to the corresponding methods in lattice, and are listed here only because they provide different defaults. See documentation for the original methods for details. darg gets passed on to density.
这些参数被传递不变，在晶格中的相应的方法，这里列出的仅仅是因为他们提供不同的默认值。有关详细信息，请参阅原始方法的文件。 darg被传递给density。
参数：overlap
The amount of overlap between stacked density plots. This argument is ignored for the flowFrame method.
重叠量之间的堆叠密度图。这种说法忽略flowFrame方法。
参数：prepanel
The prepanel function. See xyplot
prepanel功能。看到xyplot
参数：panel
the panel function. See xyplot
面板功能。看到xyplot
参数：filter
A filter, filterResult or filterResultList object or a list of such objects of the same length as the flowSet. If applicable, the gate region will be superiposed on the density curves using color shading. The software will figure out whether the filter needs to be evaluated in order to be plotted (in which case providing a filterResult can speed things up considerably).
一个filter，filterResult或filterResultList对象或相同长度的flowSet对象名单。如果适用，将门区域使用色差密度曲线superiposed。该软件将找出filter是否为了要绘制（在这种情况下提供filterResult可以加快东西大大），需要进行评估。
参数：channels
A character vector of parameters that are supposed to be plotted when the formula in x is of structure factor ~ ..
参数应该是一个特征向量绘制时的x公式结构factor ~ .。
参数：subscripts, which.channel, channel.name, y
Internal indices necessary to map panels to parameters.
必要的参数映射面板的内部指标。
参数：frames
An environment containing frame-specific data.
一个环境包含框架的具体数据。
参数：channel
The name of the currently plotted flow parameter.
目前的名称绘制流参数。
参数：col, fill, lty, lwd, alpha
Graphical parameters. These mostly exist for conveniance and much more control is available throught the lattice-like par.setting and flowViz.par.set customization. The relevant parameter category for density plots is gate.density with available parameters col, fill, lwd, alpha and lty. See flowViz.par.set for details.
图形参数。这些大多存在为conveniance和更多的控制是透过类lattice和par.setting定制flowViz.par.set。密度图的相关参数类是gate.density可用参数col，fill，lwd，alpha和lty。看到flowViz.par.set详情。
参数：groups
Use identical colors for grouping. The value of the argument is expected to be a phenotypic variable in the flowSet, or a factor.
使用相同的颜色分组。预计将在flowSet，或一个因素的表型变量的参数值。
参数：refline
Logical. Add one ore more vertical reference lines to the plot. This argument is directly passed to panel.abline.
逻辑。一矿多垂直参考线的图。此参数直接传递到panel.abline。
参数：margin
Numeric in [0,1]. Indicate margin events by horizontal bars. The value of margin is interpreted as the proportion of events on the margin over which the bars are added. E.g., a value of 0,5 means to indicate margin events if there are more than 0.5 times the total number of events. 1 means to ignore margin events completetly. For 0 bars are added even if there is only a single margin event.
数字[0,1]。保证金事件表明单杠。 margin价值将被解释为对保证金比例添加该条形的事件。例如，一个价值0,5意味着指示保证金事件，如果有0.5倍以上的事件总数。 1意味着忽视保证金事件completetly。 0条形补充说，即使是只有一个单一的保证金事件。
参数：gpar
A list of graphical parameters that are passed down to the low level panel functions. This is for internal use only. The public user interface to set graphical parameters is either par.settings for customization of a single call or flowViz.par.set for customization of session-wide defaults.
向下传递到低级别的面板功能的图形参数列表。这是仅供内部使用。公众用户界面来设置图形参数是要么定制的单一呼叫或会话范围的默认定制par.settingsflowViz.par.set。
参数：...
More arguments, usually passed on to the underlying lattice methods.
更多的参数，通常传递到底层的格子方法。
Details
详情----------Details----------
Not all standard lattice arguments will have the intended effect, but many should. For a fuller description of possible arguments and their effects, consult documentation on lattice (Trellis docs would also work for the fundamentals).
并非所有标准的晶格参数将产生预期的效果，但很多应该。一个可能的参数和它们的影响有更全面的描述，咨询文件格（文档网格，也将工作的基础）。
方法----------Methods----------
densityplot signature(x = "formula", data = "flowSet"): Creates density plots for one or several channels, with samples stacked according to a phenoData variable. Colors are used to indicate common values of this covariate across panels. Filters can be added as the optional
densityplotsignature(x = "formula", data = "flowSet")：创建一个或多个通道的密度图，根据phenoData变量堆积的样品。颜色是用来表示这个协跨板的共同价值观。过滤器可以添加可选
densityplot signature(x = "formula", data = "view"): A method to create density plots for workspace view objects. This still allows for some level of customization, but most defaults will be set depending
densityplotsignature(x = "formula", data = "view")：一个方法来创建工作区view对象的密度图。这仍然允许一些自定义的水平，但大多数默认将设置取决于
densityplot signature(x = "view", data = "missing"):
densityplotsignature(x = "view", data = "missing")：
举例----------Examples----------
data(GvHD)
GvHD <- GvHD[pData(GvHD)$Patient %in% 6:7]
densityplot(~ `FSC-H`, GvHD)
densityplot(~ `FSC-H` + `SSC-H`, GvHD)
densityplot(~ ., GvHD[1:3])
## include a filter[＃包括一个过滤器]
densityplot(~ `FSC-H`, GvHD, filter=curv1Filter("FSC-H"))
## plot a single flowFrame[＃绘制一个单一的flowFrame]
densityplot(~ `SSC-H`, GvHD[[1]], margin=FALSE)
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 18:13:25
