I have an R markdown file that I want to convert to PDF using knitr (or sweave).
For example:
---
output: pdf_document
---
```{python}
for x in range(3):
for y in range(3):
print(x+y)
```
If I knit to PDF and copy paste the for loop part back to a text editor, the tabs are gone. This is certainly expected behaviour considering how anti whitespace-preservation markdown and pdf are, but can I still somehow preserve the actual whitespace characters when knitting from R markdown to PDF?
It is not possible, there's nothing that can be done other than making sure the document looks right, i.e. visually the whitespace is there.
It comes down to what the PDF format actually is, read the accepted answer to this question - https://superuser.com/questions/198392/how-to-copy-text-out-of-a-pdf-without-losing-formatting
Related
I have a multi-page PDF document, and I want a version of the document with one of the pages in the middle with a scanned-in copy, as I needed a physical signature in the document. How can I do this with ImageMagick? I'm aware that ImageMagick may not necessarily be the best tool for the job. However, the resulting PDF does not need to be high quality or a high fidelity copy, so it should be sufficient for my needs.
As a specific example, I have a 9 page my-file.pdf, and I want to create a copy of the PDF with the 8th page replaced with page-8.png. It looks like I should be able to achieve this goal with the convert tool, though it's not immediately obvious what the syntax would be. How can I achieve this goal?
If I merely wanted to append the new page to the end of the file, I know I can do the following:
convert my-file.pdf page-8.png output-file.pdf
However, this end up with the original pages 1-9, then the new page 8. What I actually want is to replace the original page 8 with the new page 8. My desired output is:
[original pages 1 - 7],[new page 8],[original page 9]
A specific page or range of pages can be specified using the bracket syntax with zero-based indexing. For instance, [8] will refer to the ninth page, and [0-6] to the first seven pages. Using this, a duplicate of the PDF with the 8th page replaced can be achieved as follows:
convert my-file.pdf[0-6] page-8.png my-file.pdf[8] output-file.pdf
As indicated in the question, as well as a comment, Imagemagick is not a great tool for this task, as it rasterizes the output of the PDF. An alternate solution that avoids this would be to use pdftk to replace the page. While the inserted page will still be an image, the replaced pages will not be rasterized.
First, save the scanned-in page as a PDF using an application capable of this. Then, use the pdftk cat operation to combine the PDFs:
pdftk A=my-file.pdf B=page-8.pdf cat A1-7 B A9 output output-file.pdf
I thought it would be a good idea to write a longer report/protocol using bookdown since it's more comfortable to have one file per topic to write in instead of just one RMarkdown document with everything. Now I'm faced with the problem of sharing this document - the HTML looks best (except for wide tables being cut off) but is difficult to send via e-mail to a supervisor for example. I also can't expect anyone to be able to open the ePub format on their computer, so PDF would be the easiest choice. Now my problems:
My chapter headings are pretty long, which doesn't matter in HTML but they don't fit the page headers in the PDF document. In LaTeX I could define a short title for that, can I do that in bookdown as well?
I include figure files using knitr::include_graphics() inside of code chunks, so I generate the caption via the chunk options. For some figures, I can't avoid having an underscore in the caption, but that does not work out in LaTeX. Is there a way to escape the underscore that actually works (preferrably for HTML and PDF at the same time)? My LaTeX output looks like this after rendering:
\textbackslash{}begin\{figure\}
\includegraphics[width=0.6\linewidth,height=0.6\textheight]{figures/0165_HMMER} \textbackslash{}caption\{Output of HMMER for PA\_0165\}\label{fig:0165}
\textbackslash{}end\{figure\}
Edit
MWE showing that the problem is an underscore in combination with out.height (or width) in percent:
---
title: "MWE FigCap"
author: "LilithElina"
date: "19 Februar 2020"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r cars}
summary(cars)
```
## Including Plots
You can also embed plots, for example:
```{r pressure, echo=FALSE, fig.cap="This is a nice figure caption", out.height='40%'}
plot(pressure)
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
```{r pressure2, echo=FALSE, fig.cap="This is a not nice figure_caption", out.height='40%'}
plot(pressure)
```
Concerning shorter headings: pandoc, which is used for the markdown to LaTeX conversion, does not offer a "shorter heading". You can do that yourself, though:
# Really long chaper heading
\markboth{\thechapter~short heading}{}
[...]
## Really long section heading
\markright{\thesection~short heading}
This assumes a document class with chapters and sections.
Concerning the underscore in the figure caption: For me it works for both PDF and HTML to escape the underscore:
```{r pressure2, echo=FALSE, fig.cap="This is a not nice figure\\_caption", out.height='40%'}
plot(pressure)
```
I am referring to this Suppress automatic figure numbering in pdf output with r markdown/knitr
which I don't think was answered fully.
Essentially, I am using knitr::spin and rmarkdown to produce word, pdf and html documents.
For word, there appears to be no numbering when one puts in
+fig.1, fig.cap = "Figure name"
You only get an output Figure name in the caption.
To solve that, I used captioner class.
figs = captioner("Figure")
That works fine for word
But I am not faced with rewriting the script for pdf document as the caption turns up as figure 1: figure 1: The name
I am using knitr::spin to actually generate the RMD document for forward outputs in word and pdf.
I am not sure I can use hooks in knitr::spin, as I have tried it as advertised but can't get it to work.
I also tried
header-includes: \usepackage{caption} \usepackage{float}
\captionsetup[table]{labelformat=empty}
\captionsetup[figure]{labelformat=empty}
as suggested somehere to surpress the prefix for pdf but I get errors from pandoc. It uses pdf2latex.
I am not sure how one would query the output format in knitr::spin to actually produce different actions for different formats which could be a solution although cumbersome.
Thank you so much for your help from a novice.
We have to construct a postscript file that contains Arabic text, so as English text.
GhostScript shows the Arabic text correctly, but converting it to pdf does not show the Arabic letters.
PS file contains the following:
/TraditionalArabic findfont dup
length dict
copy begin
/Encoding Encoding 256 array copy def
Encoding 1 /kafinitialarabic put
Encoding 2 /behinitialarabic put
Encoding 3 /yehmedialarabic put
Encoding 4 /seenfinalarabic put
Encoding 5 /eacute put
Encoding 6 /a put
/ArabicTradDict currentdict definefont pop
end
%%Page: 1 1
%%BeginPageSetup
%%PageMedia: Color Weight Type
<< /MediaColor (Blue)/MediaWeight 75 /MediaType () /xx {2.803464567 mul} def /xx {2.83464567 mul} def /PageSize [240 xx 345 xx]>> setpagedevice
%%EndPageSetup
/ArabicTradDict 18 selectfont
72 xx 300 xx moveto
(\004\003\002\001) show
showpage
To run ghostScript: running it from command line to include all windows fonts:
gswin64.exe -sFONTPATH=%windir%/fonts -dEmbedAllFonts=true
To convert the PS file to PDF file: running the following command:
gswin64.exe -dBATCH -dNOPAUSE - sOutputFile=c:/Users/mob/Desktop/TimesNewRomanPSMT.pdf -sDEVICE=pdfwrite - dPDFSETTINGS=/prepress -dCompressFonts=false -dSubsetFonts=false -sFONTPATH=%windir%/fonts -dEmbedAllFonts=true -dEmbedAllFonts=true -f c:/Users/mob/Desktop/TimesNewRomanPSMT.ps
So when converting to PDF, the Arabic characters are not showing correctly, but showing as squares that are of no meaning...
If I use Adobe tool to convert to PDF, the PDF we get is same, except the "eacute -(005) " if included in the PS file, will show after conversion, where as when I convert with the previous command line, all characters that are added from the Encoding are not shown correctly.
Any help with that?
Thanks to KenS hints I was able to solve my problem. The encoding used wrong character names like kafinitialarabic (i mean by wrong, pdf could not understand that), everything that ended with arabic was wrong. The Traditional Arabic font does not have those names for characters. In order to know what it really understood, have converted the ttf font to afm and pfa using the following command, that is converting the true type font to type 42 font which will be understood once embed in postscript file at conversion to pdf
C:\Program Files\gs\gs9.10\bin>gswin64c.exe -dNODISPLAY -q -- ttf2pf.ps times tim
esPS timesAFM
where times is the ttf font name. I then checked the generated pfa file for the characters I wanted to add, instead of kafinitialarabic, there was kafinitial, and for kafmedialarabic there was kafmedial and so on...
It works fine now to add those in encoding, but I want to find a way instead of adding all those characters in the dictionary, I want to use the font like we use with setfont in postscript normally - if that is possible...
As already suggested, you need to ensure the glyph names you use are in the font you use, or create a new font.
I haven't found anything that will choose the correct glyph from the set of initial, medial, final, isolated, depending on context, though.
I resorted to writing a program which takes unicode arabic, reverses it the arabic characters, and then decides which tone of character to use based on it's position in a word, and whether the previous or next characters are forced into isolated or final forms. Unfortunately had to embed quite some intrinsic knowledge about the font in use and the glyph names it has, as well as typos in them, into the program.
If that's of interest, I've stuck it on github, but it's very raw and initial.
It does work, though.
https://github.com/gbjk/arabic2ps
The font I used was a traditional arabic font, with quite a few idiosyncrasies.
I am doing a massive set of file conversions and several of them happen to be ".dat" files. When I open them I see that the first line is "%!PS-Adobe". Here's an example.....
%!PS-Adobe
^M%c$in
^M/c$in {72.0 mul} def
^M%DEFINE MARGINS
^M/C$LMAR .2 c$in def %LEFT MARGIN
^M/C$RMAR 8.4 c$in def %RIGHT MARGIN
^M/C$TMAR 10.8 c$in def %TOP MARGIN
^M/C$BMAR .2 c$in def %BOTTOM MARGIN
^M/C$CF /Courier def %saves /Courier as C$CF
etc...
Am I correct in assuming that these are indeed Adobe Postscript files and ** NOT ** PDFs?
How hard is it to convert these to PDF? I was thinking command line perl via ImageMagick or something but right now I'm a little stumped about what's been handed to me.
Thank you SO Much...
Janie
You can convert these to PDF using Ghostscript and the pdfwrite device, or for simplicity the ps2pdf script supplied with Ghostscript.
Yup, that's Postscript. A PDF would start with "%PDF". If the text "^M" is literally there like that, then it was created on a Mac and got screwed up being copied to or edited on other platforms. (Maybe it was when the sample was pasted into the S.O. edit box?) It defines some variables with dollar signs in their names, which makes it look funny.
%!PS-Adobe is the signature for conforming Postscript files. (Non-conforming Postscript can get by with %!.) The signature for PDF files is %PDF-.