htmlwidgets::saveWidget Error: pandoc document conversion failed with error 97

I always use htmlwidgets::saveWidget to save my Plotly html plots in R. For some unknown reason, I started to get:

Could not find data file templates/file6efb40d38e3c.html                                        
Error: pandoc document conversion failed with error 97                                       
Execution halted

I first thought I had some problems with the temp dir so I tried to add dir.create(tempdir()) but it wasn’t it. After some more digging I found this GitHub issue and answer from cpsievert, which solved the issue.

Instead of using file=outputdir/filename.html, what I usually use to export/save everything in R, I had to split it into file=filename.html and libdir=outputdir. The error dissapeared and I could happily save my beautiful Plotly html plots.

sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: openSUSE Leap 15.0

Matrix products: default
BLAS/LAPACK: /home/joppelt/Miniconda3/envs/riboseq/lib/libopenblasp-r0.3.10.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] htmlwidgets_1.5.3

loaded via a namespace (and not attached):
[1] compiler_3.6.3    htmltools_0.5.1.1 digest_0.6.27     rlang_0.4.10

Changing font in R plots (Arial Narrow)

To my surprise, changing fonts in R plots is not a trivial task. It’s even worse if you are asked to change to font to one of the Windows licensed fonts and you are on Linux. I personally think it’s easier and faster to change the font during the editing but some people don’t know how (or don’t want to know how).

First, I tried to use the extrafont package. Even with fixes for “No FontName. Skipping” , “Error in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y”, and trying to install Windows fonts in Ubuntu, I still didn’t get the results.

The best and only solution was to use the showtext package (as found here). You will need to download the font you want. You’ll need the .tff format (.ttc, or.otf). For me, it was Arial Narrow from here.

> # Install showtext package
> install.packages("showtext")
> # Load the library and install the font
> library("showtext") 
> font_add(family = "arialn", regular = "~/Downloads/arialn.ttf")
> # Before plotting, "activate" showtext
> showtext_auto()
> # Do some fancy plots, add theme(text = element_text(family = "arialn")) to all the features where you want to use this font if you are using ggplot2, and save to PDF
> # Deactivate showtext if you no longer need it
> showtext_auto(FALSE)

And that’s it! You’ll have nice plots with the font you want.

Or, you can choose any of the Google free fonts from here. If I didn’t find Arial Narrow I would go with Archivo Narrow. In the case of Google fonts, you don’t need to download anything.

# Get the font from Google fonts
> font_add_google("Archivo Narrow", "archivon")

See more examples in the showtext readme.

But one important thing to remember – this will not store the text as text in the pdf but as curves. If you then import the pdf into a graphics editor, it won’t be easy to edit the text. You would have to convert the curves to text (somehow) and then edit it as text.

Strikethrough text in R plots

I wanted to add a strikethrough text to an R ggplot2 plot and I thought I will have to play with font settings. But, I have found this nice hint that you don’t actually have to do this. All you need is to change the encoding of the text (labels, in my case) and ggplot2 will happily do that for you. The trick is the following:

> strk <- stringr::str_replace_all("strikethrough", "(?<=.)", "\u0336")
> strk
[1] "s̶t̶r̶i̶k̶e̶t̶h̶r̶o̶u̶g̶h̶"

In reality it looks much nicer than this stupid copy-paste you see above:

Remove common part of multiple strings in R

In my work, I often get a long list of samples names which are way too long. And we all know plots don’t like long sample names. The easiest is to remove the common part of the sample names and create a shorter version. By removing the common part you only keep the unique part of the sample name which can still be used to identify the samples.

# Make a function which splits the input vector of strings (name_vect) by a separator (sepa) and returns only unique strings separated by the same separator
rename_samples <- function(name_vect, sepa) {
  samp_names.tmp <- t(as.data.frame(strsplit(name_vect, sepa, fixed = T)))
  ind <- lapply(apply(samp_names.tmp, 2, unique), length) != 1
  samp_names.tmp <- as.data.frame(samp_names.tmp[, ind])
  samp_names <- as.character(interaction(samp_names.tmp, sep = sepa))
  return(samp_names)
}

# Prepare a vector of long strings which have common parts which can be stripped
samples <- c("ath.RNASeq.MiwiKO.P30.1",
"ath.RNASeq.MiwiKO.P30.2",
"ath.RNASeq.MiwiKO.P20.1",
"ath.RNASeq.MiwiWT.P30.1",
"ath.RNASeq.MiwiWT.P30.2",
"ath.RNASeq.MiwiWT.P20.1")

# Apply the function
rename_samples(samples, ".")
[1] "MiwiKO.P30.1" "MiwiKO.P30.2" "MiwiKO.P20.1" "MiwiWT.P30.1" "MiwiWT.P30.2" "MiwiWT.P20.1"

And voila – the initial long sample names were shortened and made much nicer and cleaner.

Note: this will work only if the samples names have the same naming style. This means they have to have the same number of blocks separate by sepa character.

Remove everything after last or before first character in Bash and R

As simple as it is in Bash is not as easy in R to remove part of the string after character or even after last character.

In Bash, use can simply strip the last part of a string using:

$ var="hello.world.txt"
$ echo ${var%.*} # Remove all after last "."
hello.world
$ echo ${var%%.*} # Remove all after first "."
hello
$ echo ${var#*.} # Remove all before first "."
world.txt 
$ echo ${var##*.} # Remove all before last "."
txt

In R is a bit more complicated (unless you want to use special packages such as stringr). To do the same in R these are the commands you would have to use:

> vari <- "hello.world.txt"
> sub(".[^.]+$", "", vari) # Remove all after last "."
hello.world
> gsub("\\..*", "", vari) # Remove all after first "."
hello
> sub(".*?\\.", "", vari) # Remove all before first "."
world.txt 
> gsub(".*\\.","",vari) # Remove all before last "."
txt