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tilschaef / scRNA-seq

From fastq to preprocessed counttable (for in-house CELSeq2 method), with Kallisto | Bustools workflow.
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Output to pdf #3

Closed Rebecza closed 3 years ago

Rebecza commented 3 years ago

Concerning: .rmd -> .pdf

I really like the pdf output, it is overall really nice!! (: (also the contents at the top, looks faancy)

There are some spots where the lines are going outside the page width, see below for an example.

Is there a fix for this maybe (a wrapping setting)? Or does this need selection of the long lines in the rmd where this happens? It also sometimes happens in code chunks.

afbeelding

tilschaef commented 3 years ago

That seems to be related to the way how the pdf is generated via pandoc since it's first converted to a latex document and then to pdf. The default environment does not break up long lines of text. However, it can be fixed by adding a custom preamble.tex file and include it in the document definition (https://bookdown.org/yihui/rmarkdown-cookbook/text-width.html). The pdf layout and code highlightning is now a bit different but clearer in my opinion. I added it in https://github.com/tilschaef/scRNA-seq/commit/f9c9fa20c6b239b03bb99fcd85dbf4dfa887f379

tilschaef commented 3 years ago