动画RGL图与knitr [英] Animated rgl graphs with knitr

问题描述

我想通过 knitr <包括动画 RGL 图我的 .Rnw 文件/ code>。这里是我的MWE：

I want to include animated rgl graphs in my .Rnw document through knitr. Here is my MWE:

\documentclass{article}

<< label = setup, include = FALSE>>=
opts_chunk$set(fig.path = 'figure/',  cache = FALSE, dev = "pdf",  fig.align = 'center', fig.show = 'hold', fig.width = 3, fig.height = 3,  echo = TRUE, warning = FALSE, message = FALSE, size = 'footnotesize', comment=NA, results='hold')

knit_hooks$set(par = function(before, options, envir){
if (before && options$fig.show!='none')
 par(mar = c(4, 4, 0.1, 0.1), cex.lab = 0.95, cex.axis = 0.9, mgp = c(2, 0.7, 0), tcl = -0.3)
}
)
knit_hooks$set(rgl = function(before, options, envir) {
  if (!before) {
    ## after a chunk has been evaluated
    if (rgl.cur() == 0) return()  # no active device
    name = paste(options$fig.path, options$label, sep = '')
    rgl.snapshot(paste(name, '.png', sep = ''), fmt = 'png')
    return(paste('\\includegraphics{', name, '}\n', sep = ''))
  }
}
)

options(replace.assign = TRUE, width = 60)
@ 
\begin{document}

<< label=packages >>=
library(car)
@
<< label=rgl1, rgl=TRUE, fig.show='animate' >>=
scatter3d(prestige ~ income + education, data=Duncan)
@

\end{document}

我没有在我的文档针织越来越图表。任何帮助将是非常美联社preciated。谢谢

I'm not getting graph in my knitted documents. Any help will be highly appreciated. Thanks

我仍然无法得到它的工作，并得到以下警告：

I'm still unable to get it work and getting the following warning:

Warning messages:
1: In rgl.snapshot(paste(name, ".png", sep = ""), fmt = "png") :
  RGL: Pixmap save: unable to open file 'D:\A B\C D UAF\Test\knitr\rglAnimation\figure\rgl1.png' for writing
2: In rgl.snapshot(paste(name, ".png", sep = ""), fmt = "png") :
  snapshot failed
3: running command '"C:\PROGRA~2\MIKTEX~1.9\miktex\bin\x64\texi2dvi.exe" --quiet --pdf "rglAnimation.tex" --max-iterations=20 -I "C:/PROGRA~1/R/R-31~1.1/share/texmf/tex/latex" -I "C:/PROGRA~1/R/R-31~1.1/share/texmf/bibtex/bst"' had status 1 

我的 sessionInfo（）是

R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] mgcv_1.8-2    nlme_3.1-117  rgl_0.93.1098 car_2.0-21    knitr_1.6.15 

loaded via a namespace (and not attached):
[1] evaluate_0.5.5  formatR_1.0     grid_3.1.1      highr_0.3      
[5] lattice_0.20-29 MASS_7.3-34     Matrix_1.1-4    nnet_7.3-8     
[9] stringr_0.6.2  

编辑

在<$ C $更改 fig.path ='图/到 fig.path ='' C> opts_chunk $集编译与图文档>，但没有任何动画。极力AP preciate如果一些指导我如何获得动画 RGL 图表与 fig.path ='图/。谢谢

Changing fig.path = 'figure/' to fig.path = '' in opts_chunk$set compiles the document with png graphs but without any animation. Would highly appreciate if some guide me how to get animated rgl graphs with fig.path = 'figure/'. Thanks

推荐答案

我已经有了基于该作品使用knitr在Windows 8.1中RStudio 0.99.441你一个例子。

I've got an example based on yours that works using knitr on Windows 8.1 within RStudio 0.99.441.

这会产生积的40帧动画。它使用内置的 hook_plot_custom 来包括被动画3D图手动生成的地块。动画的code是基于那些在 play3d 和 movie3d 的帮助和来源。 movied3d 本身不能使用，因为它是在它的文件命名太执着。

This produces a 40-frame animation of the plot. It uses the built-in hook_plot_custom to include the plots which are generated manually by animating the 3d plot. The code for the animation was based on those in the help and source of play3d and movie3d. movied3d itself cannot be used because it is too inflexible in its file naming.

我在 https://github.com/NikNakk/testAnimateRgl/。 PDF格式是 https://github.com/NikNakk/testAnimateRgl/raw/master /rglKnitr.pdf

I've put this up on github at https://github.com/NikNakk/testAnimateRgl/ . The pdf is at https://github.com/NikNakk/testAnimateRgl/raw/master/rglKnitr.pdf

\documentclass{article}
\usepackage{animate}

<< label = setup, include = FALSE>>=
library("rgl")
library("car")
library("knitr")
knit_hooks$set(rgl = hook_plot_custom)
@ 
\begin{document}

<< label=rgl1, rgl=TRUE, fig.show='animate', fig.width=5, fig.height=5, out.width='.6\\linewidth', dev='png', fig.num = 40, interval=0.1>>=
scatter3d(prestige ~ income + education, data=Duncan)
M <- par3d("userMatrix")
par3d(windowRect = 100 + opts_current$get("dpi") *
        c(0, 0, opts_current$get("fig.width"), 
        opts_current$get("fig.height")))
spinFunc <- par3dinterp(userMatrix=list(M,
                             rotate3d(M, pi/2, 1, 0, 0),
                             rotate3d(M, pi/2, 0, 1, 0)))
for(i in 1:40) {
  par3d(spinFunc(i / 10))
  Sys.sleep(0.05)
  rgl.snapshot(fig_path(".png", number = i), fmt = "png")
}
@

\end{document}

编辑：新版

下面是另一个这表明使用定制块选项来设置的参数相当简单 spin3d 版本。请注意，这个版本中，块是只是一个单一的线（ scatter3d 图）。 spin3d.axis 用来轴参数设置为 spin3d ; spin3d.rpm 用来设置转参数。图像和图像之间的时间间隔数是使用标准的 fig.num 和间隔参数进行设置。

Here's another version which demonstrates the use of custom chunk options to set the parameters for the rather simpler spin3d. Note that with this version, the chunk is just a single line (the scatter3d plot). spin3d.axis is used to set the axis parameter to spin3d; spin3d.rpm is used to set the rpm parameter. The number of images and the interval between images is set using the standard fig.num and interval parameters.

\documentclass{article}
\usepackage{animate}

<< label = setup, include = FALSE>>=
  library("rgl")
library("car")
library("knitr")
hook_rgl_spin <- function(before, options, envir) {
  if (!before) {
    par3d(windowRect = 100 + options$dpi *
          c(0, 0, options$fig.width, 
            options$fig.height))
    if (!is.null(options$spin3d.axis)) {
      spin3d.axis <- options$spin3d.axis
    } else {
      spin3d.axis <- c(0, 0, 1)
    }
    if (!is.null(options$spin3d.rpm)) {
      spin3d.rpm <- options$spin3d.rpm
    } else {
      spin3d.rpm <- c(0, 0, 1)
    }
    spinFunc <- spin3d(axis = spin3d.axis, rpm = spin3d.rpm)
    for(i in 1:options$fig.num) {
      par3d(spinFunc(i * options$interval))
      Sys.sleep(0.05)
      rgl.snapshot(fig_path(".png", number = i), fmt = "png")
    }

    hook_plot_custom(before, options, envir)
  }
}
knit_hooks$set(rgl = hook_rgl_spin)
@ 
  \begin{document}

<< label=rgl1, rgl=TRUE, fig.show='animate', fig.width=5, fig.height=5, out.width='.6\\linewidth', dev='png', fig.num = 40, interval=0.1, spin3d.axis=c(0, 0, 1), spin3d.rpm = 20>>=
  scatter3d(prestige ~ income + education, data=Duncan)
@

  \end{document}

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