动画rgl图形与knitr

Question

我想通过knitr在我的.Rnw文档中包含动画rgl图形。这是我的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}

我在我的针织文档中没有得到图形。

更新

我仍然无法让它工作，并得到以下警告:

Warning messages:
1: In rgl.snapshot(paste(name, ".png", sep = ""), fmt = "png") :
  RGL: Pixmap save: unable to open file 'D:A BC D UAFTestknitrrglAnimationfigurergl1.png' for writing
2: In rgl.snapshot(paste(name, ".png", sep = ""), fmt = "png") :
  snapshot failed
3: running command '"C:PROGRA~2MIKTEX~1.9miktexbinx64texi2dvi.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  

在opts_chunk$set中将fig.path = 'figure/'更改为fig.path = ''将编译具有png图形但没有任何动画的文档。如何使用fig.path = 'figure/'获得动画rgl图形

Answer 1

我有一个基于你的例子，在RStudio 0.99.441的Windows 8.1中使用knitr。

这将生成一个40帧的情节动画。它使用内置的hook_plot_custom来包括通过动画3d情节手动生成的情节。动画的代码是基于play3d和movie3d的帮助和源代码。movied3d本身不能使用，因为它的文件命名太不灵活了。

我把这个放在github上https://github.com/NikNakk/testAnimateRgl/。pdf在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:新版本

下面是另一个版本，它演示了使用自定义块选项来为相当简单的spin3d设置参数。注意，在这个版本中，块只有一行(scatter3d图)。spin3d.axis用于设置轴参数为spin3d;spin3d.rpm用于设置rpm参数。使用标准的fig.num和interval参数设置图像的数量和图像之间的间隔。

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}