[R] Plots in ioslides and R markdown

[Duncan Murdoch]

On 26/08/2018 4:40 AM, Patrick Connolly wrote:
> On Sat, 25-Aug-2018 at 08:10PM -0400, Duncan Murdoch wrote:
> 
> |> On 25/08/2018 7:37 PM, Patrick Connolly wrote:
> |> >On Sat, 25-Aug-2018 at 07:53AM -0400, Duncan Murdoch wrote:
> |> >
> |> >|> On 25/08/2018 6:21 AM, Patrick Connolly wrote:
> |> >|> >---
> |> >|> >title: "Barking up the wrong tree"
> |> >|> >author: "Patrick Connolly"
> |> >|> >date: "`r format(Sys.time(), '%a %d/%m/%Y %H:%M')`"
> |> >|> >output:
> |> >|> >   ioslides_presentation: default
> |> >|> >   slidy_presentation: default
> |> >|> >   beamer_presentation: default
> |> >|> >---
> |> >|> >
> |> >|> >```{r global_options, echo=FALSE}
> |> >|> >knitr::opts_chunk$set(tidy=TRUE,
> |> >|> >                       warning=FALSE,
> |> >|> >                       message=FALSE,
> |> >|> >                       cache=FALSE,
> |> >|> >                       dpi = 300)
> |> >|>
> |> >|> Drop the dpi setting and it will work fine.
> |> >
> |> >Still doesn't avoid what I think is the issue with Cairo
> |> >
> |> >    Error in axis(side = side, at = at, labels = labels, ...) : X11
> |> >   font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 1 at size 12
> |> >   could not be loaded Calls: <Anonymous> ... plot.default -> localAxis
> |> >   -> Axis -> Axis.default -> axis
> |> >
> |> >   Execution halted
> |> >
> |> >
> |> >For interactive plotting, Rstudio plots those 6 plots on one page so
> |> >no issue is apparent, as it will if I use a pdf device within ESS.
> |>
> |> So use RStudio, don't use ESS.
> 
> I'm using Rstudio to try to output ioslides which runs into the font
> problem which doesn't arise when plotting to the plot pane.  RStudio's
> no advantage when the objective is ioslides.  That observation gives
> rise to my hypothesis that to produce ioslides, Cairo is utilized in
> ways incomprehensible to me.

Since that error happens during the axis() call, it's related to the 
graphics device that is being used.  That would be different for an 
ioslides document than it is for interactive display.  On my system (and 
I think on all systems) the png() device is used for ioslides.

If you run debug(png) then rmarkdown::render( <your Rmd file> ), you'll 
see what options are being passed to png.  On my system, it is called 
with no arguments except a filename, so it uses the defaults for all 
other arguments.  That means the "type" argument eventually gets set to 
"quartz".  Yours will be different, but I don't know what it will get. 
Maybe you can choose something different than the default by setting 
options("bitmapType").

Duncan Murdoch
> 
> |>
> |> >However, when plotting interactively in ESS, a basic font is used for
> |> >the labels which is OK for preliminary quick look.  No error message
> |> >is shown, but I suspect that it is defaulting to a crude font because
> |> >the helvetica font is not available.
> |> >
> |> >It appears to me that the font problem doesn't arise with Rstudio
> |> >unless the desired output is ioslides.  Which brings us back to the
> |> >issue with Cairo.  There are lots of hits when I search for
> |> >configuring fonts, Cairo and R but I've not found anything I can use.
> |> >
> |>
> |> I don't see a font problem in MacOS.  I don't think you've stated
> |> what system you are using (but I may have missed it).
> 
> It has something to do with X11 which I guess MacOS doesn't use.
> 
>> sessionInfo()
> R version 3.5.0 (2018-04-23)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 14.04.5 LTS
> 
> Matrix products: default
> BLAS: /home/pat/local/R-3.5.0/lib/libRblas.so
> LAPACK: /home/pat/local/R-3.5.0/lib/libRlapack.so
> 
> locale:
>   [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8
>   [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8
>   [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] utils     stats     grDevices graphics  methods   base
> 
> other attached packages:
> [1] lattice_0.20-35
> 
> loaded via a namespace (and not attached):
>   [1] Rcpp_0.12.17     bindr_0.1.1      magrittr_1.5     tidyselect_0.2.4
>   [5] munsell_0.5.0    colorspace_1.3-2 xtable_1.8-2     R6_2.2.2
>   [9] rlang_0.2.1      plyr_1.8.4       dplyr_0.7.6      tools_3.5.0
> [13] grid_3.5.0       htmltools_0.3.6  crosstalk_1.0.0  leaflet_2.0.1
> [17] assertthat_0.2.0 digest_0.6.15    tibble_1.4.2     bindrcpp_0.2.2
> [21] shiny_1.1.0      purrr_0.2.5      later_0.7.3      htmlwidgets_1.2
> [25] promises_1.0.1   glue_1.2.0       mime_0.5         compiler_3.5.0
> [29] pillar_1.2.3     scales_0.5.0     httpuv_1.4.4.2   pkgconfig_2.0.1
> 
> 
> |>
> |> Duncan Murdoch
> |>
> |> >I would appreciate pointers where I can find useful information.
> |> >
> |> >Thank you.
> |> >
> |> >|>
> |> >|> Duncan Murdoch
> |> >|>
> |> >|> >```
> |> >|> >## 6 different Regression Trees
> |> >|> >
> |> >|> >```{r 6 different Regression Trees, echo = FALSE, messages=FALSE, fig.width = 7, fig.height = 5}
> |> >|> >
> |> >|> >  par(mfrow = c(2, 3))
> |> >|> >plot(1:10)
> |> >|> >plot(12:4)
> |> >|> >plot(seq(0, 800))
> |> >|> >plot(-100:-900)
> |> >|> >plot(12:50)
> |> >|> >plot(90:54)
> |> >|> >```
> |> >
>