Jandre Marais Jandre Marais - 3 months ago 17
R Question

Side-by-side rgl plots with R Markdown

I am trying to get two 3D scatter plots, drawn with the rgl package, side-by-side in an R Markdown document. For example:

mfrow3d(nr = 1, nc = 2, sharedMouse = TRUE)
plot3d(mtcars[, 1:3], type = "s")
plot3d(mtcars[, 4:6], type = "s")
rglwidget()


This works perfectly when run directly in the console but when knit to an HTML document using R Markdown, it seems as if only the second plot is rendered.

I tried adding
knit_hooks$set(webgl = hook_webgl)
and setting the chunk option
webgl = TRUE
, but that did not help either.

Any suggestions would be appreciated.

This is my output from
sessionInfo()
:

R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

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

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

other attached packages:
[1] rgl_0.96.0 tidyr_0.6.0 dplyr_0.5.0 smacof_1.8-13
[5] emojifont_0.3.3 gridExtra_2.2.1 knitr_1.14 MASS_7.3-45
[9] shinydashboard_0.5.1 shiny_0.13.2 RColorBrewer_1.1-2 ggplot2_2.1.0

loaded via a namespace (and not attached):
[1] gtools_3.5.0 splines_3.3.1 lattice_0.20-33 colorspace_1.2-6
[5] htmltools_0.3.5 yaml_2.1.13 base64enc_0.1-3 chron_2.3-47
[9] survival_2.39-4 DBI_0.5 foreign_0.8-66 plyr_1.8.4
[13] stringr_1.1.0 munsell_0.4.3 gtable_0.2.0 htmlwidgets_0.7
[17] evaluate_0.9 latticeExtra_0.6-28 httpuv_1.3.3 proto_0.3-10
[21] Rcpp_0.12.6 acepack_1.3-3.3 xtable_1.8-2 polynom_1.3-8
[25] scales_0.4.0 formatR_1.4 showtext_0.4-4 gdata_2.17.0
[29] jsonlite_1.0 Hmisc_3.17-4 sysfonts_0.5 mime_0.5
[33] weights_0.85 digest_0.6.10 stringi_1.1.1 showtextdb_1.0
[37] grid_3.3.1 tools_3.3.1 magrittr_1.5 tibble_1.2
[41] Formula_1.2-1 mice_2.25 cluster_2.0.4 Matrix_1.2-6
[45] rsconnect_0.4.3 data.table_1.9.6 nnls_1.4 assertthat_0.1
[49] rmarkdown_1.0.9013 R6_2.1.3 rpart_4.1-10 nnet_7.3-12

Answer

There seems to be at least one, and more like two bugs in play here. Modifying your code a bit, this:

```{r echo=T}
library(rgl)
library(rglwidget)
library(knitr)
knit_hooks$set(webgl = hook_webgl)

mfrow3d(nr = 2, nc = 2, sharedMouse = T)  
plot3d(mtcars[, 1:3], type = "s",)  
plot3d(mtcars[, 4:6], type = "s")
plot3d(mtcars[, 1:3], type = "s")  
plot3d(mtcars[, 4:6], type = "s")
rglwidget()
```

produces this in a briefly visible device window:

enter image description here

but this in the R-Studio preview window:

enter image description here

And this in the html file loaded into the Chrome browser:

enter image description here

So only the first one works, and markdown seems to break it.

I would say you should probably just avoid composing multiple rgl plots in markdown until this (these) bugs get fixed. Might be hard as it seems to be some weird interaction between the various graphics devices and the library.

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