17

我正在为 R6 类及其方法的文档而苦苦挣扎。我的目标是在 RStudio 中自动完成这些方法。目前，我只得到方法的名称，但没有我通常使用roxygen2记录带有参数的函数等获得的帮助信息。

目前，这是我的课：

#' @importFrom R6 R6Class
MQParameters <- R6::R6Class(
  'MQParameters',
  public=list(
    initialize=function(file_path=NA) {
      private$location <- file_path
      mq_parameters <- read.delim(file_path, stringsAsFactors=FALSE)
      mq_parameters <-
        setNames(mq_parameters$Value, mq_parameters$Parameter)
      private$mq_version <- unname(mq_parameters['Version'])
      private$fasta_file <-
        gsub('\\\\', '/', strsplit(mq_parameters['Fasta file'], ';')[[1]])
    },
    # this method returns the version
    getVersion=function() {
      private$mq_version
    },
    # this methods returns the fastafile.
    # @param new_param it is possible to rewrite the basedir.
    getFastaFile=function(new_basedir=NA) {
      if(is.na(new_basedir)) {
        private$fasta_file
      } else {
        file.path(new_basedir, basename(private$fasta_file))
      }
    }
  ),
  private=list(
    location=NULL,
    mq_version=NULL,
    fasta_file=NULL
  )
)

如果你有兴趣测试这个类，这里​​有一个可重现的小例子：

df <- data.frame(Parameter=c('Version', 'Fasta file'),
                 Value=c('1.5.2.8','c:\\a\\b.fasta'))
write.table(df, 'jnk.txt', sep='\t', row.names=F)

p <- MQParameters$new('jnk.txt')
p$getVersion()
# [1] "1.5.2.8"
p$getFastaFile()
# [1] "c:/a/b.fasta"
p$getFastaFile(new_basedir='.')
# [1] "./b.fasta"

我不知道如何记录参数，因为参数实际上属于创建者而不属于类。函数中其他方法的参数呢？
用它的方法记录一个类的首选方法是什么？

我很想从 RStudio 获得“正常”功能，比如F1直接进入帮助页面。

通过搜索互联网，我已经在 Github 上看到了一些关于这个话题的报道，但它们已经有一年多的历史了。

更新

多亏了我的回答，mikeck我现在有了一个很好的类文档及其方法。但是我仍然缺乏的是获得函数/方法的提示及其参数的可能性，就像这个屏幕截图中的一个通用函数：

rStudio 函数帮助

我想知道我是否可以以某种方式手动注册我的函数，但由于它没有特定的名称（它总是与您用于对象的变量 objectname 耦合OBJECTNAME$methodeCall()）我不知道该怎么做。

4

2 回答 2

12

我的理解是，用与你的类NULL相同的对象来记录一个对象是最容易的@name，因为这提供了最大的灵活性。我在我的一个包中使用了 R6 类；你可以在这里查看 roxygen 。我在下面包含了一个小样本：

#' Python Environment
#' 
#' The Python Environment Class. Provides an interface to a Python process.
#' 
#' 
#' @section Usage:
#' \preformatted{py = PythonEnv$new(port, path)
#'
#' py$start()
#' 
#' py$running
#' 
#' py$exec(..., file = NULL)
#' py$stop(force = FALSE)
#' 
#' }
#'
#' @section Arguments:
#' \code{port} The port to use for communication with Python.
#' 
#' \code{path} The path to the Python executable.
#' 
#' \code{...} Commands to run or named variables to set in the Python process.
#'
#' \code{file} File containing Python code to execute.
#' 
#' \code{force} If \code{TRUE}, force the Python process to terminate
#'   using a sytem call.
#' 
#' @section Methods:
#' \code{$new()} Initialize a Python interface. The Python process is not 
#'   started automatically.
#'   
#' \code{$start()} Start the Python process. The Python process runs 
#'   asynchronously.
#'
#' \code{$running} Check if the Python process is running.
#'   
#' \code{$exec()} Execute the specified Python 
#'   commands and invisibly return printed Python output (if any).
#'   Alternatively, the \code{file} argument can be used to specify
#'   a file containing Python code. Note that there will be no return 
#'   value unless an explicit Python \code{print} statement is executed.
#' 
#' \code{$stop()} Stop the Python process by sending a request to the 
#'   Python process. If \code{force = TRUE}, the process will be 
#'   terminated using a system call instead.
#'
#' @name PythonEnv
#' @examples
#' pypath = Sys.which('python')
#' if(nchar(pypath) > 0) { 
#'   py = PythonEnv$new(path = pypath, port = 6011)
#'   py$start()
#'   py$running
#'   py$stop(force = TRUE)
#' } else 
#' message("No Python distribution found!")
NULL

#' @export
PythonEnv = R6::R6Class("PythonEnv", cloneable = FALSE,
  # actual class definition...

还有其他替代（但类似）实现；此示例使用@docType class可能更适合您的方法：

#' Class providing object with methods for communication with lightning-viz server
#'
#' @docType class
#' @importFrom R6 R6Class
#' @importFrom RCurl postForm
#' @importFrom RJSONIO fromJSON toJSON
#' @importFrom httr POST
#' @export
#' @keywords data
#' @return Object of \code{\link{R6Class}} with methods for communication with lightning-viz server.
#' @format \code{\link{R6Class}} object.
#' @examples
#' Lightning$new("http://localhost:3000/")
#' Lightning$new("http://your-lightning.herokuapp.com/")
#' @field serveraddress Stores address of your lightning server.
#' @field sessionid Stores id of your current session on the server.
#' @field url Stores url of the last visualization created by this object.
#' @field autoopen Checks if the server is automatically opening the visualizations.
#' @field notebook Checks if the server is in the jupyter notebook mode.
#' #' @section Methods:
#' \describe{
#'   \item{Documentation}{For full documentation of each method go to https://github.com/lightning-viz/lightining-r/}
#'   \item{\code{new(serveraddress)}}{This method is used to create object of this class with \code{serveraddress} as address of the server object is connecting to.}
#'
#'   \item{\code{sethost(serveraddress)}}{This method changes server that you are contacting with to \code{serveraddress}.}
#'   \item{\code{createsession(sessionname = "")}}{This method creates new session on the server with optionally given name in \code{sessionname}.}
#'   \item{\code{usesession(sessionid)}}{This method changes currently used session on the server to the one with id given in \code{sessionid} parameter.}
#'   \item{\code{openviz(vizid = NA)}}{This method by default opens most recently created by this object visualization. If \code{vizid} parameter is given, it opens a visualization with given id instead.}
#'   \item{\code{enableautoopening()}}{This method enables auto opening of every visualisation that you create since that moment. Disabled by default.}
#'   \item{\code{disableautoopening()}}{This method disables auto opening of every visualisation that you create since that moment. Disabled by default.}
#'   \item{\code{line(series, index = NA, color = NA, label = NA, size = NA, xaxis = NA, yaxis = NA, logScaleX = "false", logScaleY = "false")}}{This method creates a line visualization for vector/matrix with each row representing a line, given in \code{series}.}
#'   \item{\code{scatter(x, y, color = NA, label = NA, size = NA, alpha = NA, xaxis = NA, yaxis = NA)}}{This method creates a scatterplot for points with coordinates given in vectors \code{x, y}.}
#'   \item{\code{linestacked(series, color = NA, label = NA, size = NA)}}{This method creates a plot of multiple lines given in matrix \code{series}, with an ability to hide and show every one of them.}
#'   \item{\code{force(matrix, color = NA, label = NA, size = NA)}}{This method creates a force plot for matrix given in \code{matrix}.}
#'   \item{\code{graph(x, y, matrix, color = NA, label = NA, size = NA)}}{This method creates a graph of points with coordinates given in \code{x, y} vectors, with connection given in \code{matrix} connectivity matrix.}
#'   \item{\code{map(regions, weights, colormap)}}{This method creates a world (or USA) map, marking regions given as a vector of abbreviations (3-char for countries, 2-char for states) in \code{regions} with weights given in \code{weights} vector and with \code{colormap} color (string from colorbrewer).}
#'   \item{\code{graphbundled(x, y, matrix, color = NA, label = NA, size = NA)}}{This method creates a bundled graph of points with coordinates given in \code{x, y} vectors, with connection given in \code{matrix} connectivity matrix. Lines on this graph are stacked a bit more than in the \code{graph} function.}
#'   \item{\code{matrix(matrix, colormap)}}{This method creates a visualization of matrix given in \code{matrix} parameter, with its contents used as weights for the colormap given in \code{colormap} (string from colorbrewer).}
#'   \item{\code{adjacency(matrix, label = NA)}}{This method creates a visualization for adjacency matrix given in \code{matrix} parameter.}
#'   \item{\code{scatterline(x, y, t, color = NA, label = NA, size = NA)}}{This method creates a scatterplot for coordinates in vectors \code{x, y} and assignes a line plot to every point on that plot. Each line is given as a row in \code{t} matrix.}
#'   \item{\code{scatter3(x, y, z, color = NA, label = NA, size = NA, alpha = NA)}}{This method creates a 3D scatterplot for coordinates given in vectors \code{x, y, z}.}
#'   \item{\code{image(imgpath)}}{This method uploads image from file \code{imgpath} to the server and creates a visualisation of it.}
#'   \item{\code{gallery(imgpathvector)}}{This method uploads images from vector of file paths \code{imgpathvector} to the server and creates a gallery of these images.}}


Lightning <- R6Class("Lightning",
...
)

编辑

如果您正在寻找一种在尝试使用类方法时显示 RStudio 工具提示的方法......不幸的是，我认为您不会找到不需要以消除类的方式对类进行编码的解决方案R6 类的便利性和功能性。

@f-privé 提供了一个答案，可以满足您的要求——只需将该逻辑扩展到所有方法即可。例如，myclass$my_method改为由

my_method = function(r6obj) {
  r6obj$my_method()
}
obj$my_method()
my_method(obj)      # equivalent

换句话说，您需要为每个方法创建一个包装器。这显然不如仅使用 来编程方便obj$my_method()，并且可能首先扼杀了使用 R6 类的用处。

这里的问题实际上是 RStudio。IDE 没有通过分析代码来识别 R6 类的好方法，并且无法区分已定义类的方法和列表或环境的元素。此外，RStudio 无法为任意函数提供帮助，例如：

na.omit()         # tooltip shows up when cursor is within the parentheses
foo = na.omit
foo()             # no tooltip

这非常类似于调用特定 R6 对象的方法。

于 2017-08-10T01:25:17.783 回答
7

我认为 R 人不想$new(...)用来获取新类的实例。他们更喜欢使用与类同名的函数来构造它的实例。

所以，你可以做的是重命名你的 R6ClassGeneratorMQParameters_R6Class并创建另一个函数

MQParameters <- function(file_path = NA) {
  MQParameters_R6Class$new(file_path)
}

然后，将此函数记录为任何其他函数，您将从 RStudio 获得“显示函数调用及其参数的黄色小窗口”。和快乐的 R 用户。

于 2017-08-14T14:15:28.827 回答