I read such an example in 10 minutes in pandas
#+begin_src ipython :session alinbx :results raw drawer
ts = pd.Series(np.random.randn(1000),
index=pd.date_range('1/1/2000', periods=1000))
ts = ts.cumsum()
ts.plot()
#+end_src
get the result:
The image displayed is very tiny, how could enlarge the it by modifying the ipython's configuration?
Related
I would like to use reveal-code-focus within org-mode in Emacs (https://bnjmnt4n.github.io/reveal-code-focus/#/reveal-code-focus). Is there an example that someone could walk me through on how to do it? I have looked and looked but not found any help.
#+BEGIN_SRC python :results output
import random
random.seed(1)
print("Hello World! Here's a random number: %f" % random.random())
#+END_SRC
In the above example I want the background color for random.seed(1) to be highlighted when exporting to HTML using reveal.js.
Please note that, it is not for syntax highlighting but for code focus.
In emacs org-mode, is it possible to apply markup to the RESULTS section of a SRC block output when exporting to PDF (or any export format)?
For example, here is a src code block:
#+BEGIN_SRC python :results output :exports both
print '*I would like this line to be bold*'
#+END_SRC
#+RESULTS:
: *I would like this line to be bold*
The RESULTS section is generated by the usual C-c C-c.
Normally org-mode will mark up text in * as bold, but it obviously doesn't do this if that text is in a RESULTS block (or, it appears in a SRC block). In my example, if I export this (PDF via Latex) then I just get the exact output of
*I would like this line to be bold*
...there's no markup.
Answering my own question.
There are formatting modifiers you can add in the header section of the SRC block to do what I want. One of them is 'raw'.
#+BEGIN_SRC python :results output raw
print '*I would like this line to be bold*'
#+END_SRC
#+RESULTS:
*I would like this line to be bold*
(Ironically on Stack Overflow I'm not sure how to mix code blocks and bold face, but the bold line is the result of running the code block in org-mode).
There is a full list of ways to format output here:
http://orgmode.org/manual/results.html#results
I am thinking about writing my thesis with rmarkdown and latex. I'm getting the hang of how it all works, however, when I try to add a figure (not an R plot) to the text and render it to pdf, the caption and in-text reference dissappear.
This is the code snippet I use to add a figure:
---
title: "Untitled"
output: pdf_document
---
see figure \ref{fig1}.
This is what knitr creates:
This is what pandoc creates:
Question:
How do I make figure captions and in-text references to those figures in Rmarkdown that will display when rendered to pdf?
OR
How do I tell pandoc what Rmarkdown is so it will render R code and plots?
Please see the documentation of R Markdown for PDF output, and in particular, look for fig_caption. Figure captions are turned off by default in R Markdown, and you have to turn them on (fig_caption: true). You can also find this setting from the gear button on the toolbar of RStudio IDE.
Update: please check https://github.com/yihui/knitr/issues/1063.
Question: How do I make figure captions and in-text references to those figures in Rmarkdown that will display when rendered to pdf?
To get the cross-reference in the PDF produce by LaTeX you need to run LaTeX more than once. Some LaTeX IDE does it for you.
knitr is only running LaTeX once and that is the reason that you only get ??. To confirm that this was the problem I ran
library(knitr)
knitr()
in R that returned
see figure \ref{fig1}.
\begin{figure}[htbp]
\centering
\includegraphics{imagem.jpg}
\caption{picture \label{fig1}}
\end{figure}
which is a valid LaTeX code.
How do I tell pandoc what Rmarkdown is so it will render R code and plots?
Pandoc only understand Markdown (not RMarkdown). First you have to call knitr to generate the Markdown from the RMarkdown and after it call Pandoc to convert the Markdown to LaTeX.
I just found a very useful solution here.
First, include the following chunk:
```{r functions, include=FALSE}
# A function for captioning and referencing images
fig <- local({
i <- 0
ref <- list()
list(
cap=function(refName, text) {
i <<- i + 1
ref[[refName]] <<- i
paste("Figure ", i, ": ", text, sep="")
},
ref=function(refName) {
ref[[refName]]
})
})
```
After, we can add the caption of the figure/table in the figure chunk options like:
```{r, fig.cap=paste("Your caption.")}
See that fig.cap works better with paste.
In Rmarkdown
for markdown figures
{figure dimensions}
# how to cite markdown figure
\ref{labelx}
for latex figures
Add following in the figure environment of latex which starts with
\begin{figure}
includegraphics[]{/path to figure}
\label{label}
\end{figure}
# how to cite latex
\ref{label}
for bookdown
add chunk names as label names like
{r label2,echo=F}
# to cite by using bookdown use
\#ref(fig:label2)
similarly for tab we cite table as \#ref(tab:table_label)
For captioner package
add a chunk at the top of rmarkdown document
tab_cap <- captioner(prefix = "table")
fig_cap <- captioner(prefix = "figure")
where prefix is the prefix for cross referencing a figure.
add this in chunk options
{r fig_cap("labelforcaptioner","caption for captioner figure"}
note that fig_cap is similar to fig_cap in chunk code for captioner.
and to cite use
`r fig_cap("label4",display='cite')
I use org-mode+LaTex to take scientific notes and produce them to PDFs, I can use
#+BEGIN_src latex:
\begin{equation}
\int_\text{Birth}^{Death} work \mathrm{d} t = \text{LIFT}
\end{equation}
#+END_src
to highlight all latex codes between codes #+BEGIN_src latex .... #+END but if I don't delete this codes before I produce my org-document to PDF, I will get the unexpected #+BEGIN_src latex and #+END in the PDF.
Is there a more convenient way that can make latex syntax highlighted in org-mode with no unexpected codes left in PDF?
I searched some info about highlight source codes in org-mode, however, it seem no one concerns my demand that I simply only need the function of highlights of the latex syntax to make me edit easily, not the highlights in the resulting PDF.
Thanks a lot.
The (first?) problem is the colon after "latex" on the first line.
I'm aware of the %load function (formerly %loadpy) which loads the contents of a file (or URL, ...) into a new input cell (which can be executed afterwards).
I'm also aware of %less, %more and %pycat, which show the contents of a file in a pager (which means in the notebook it's shown in the split-window at the bottom of the screen).
Is there a (magic) command to load a file and show its content (with syntax highlighting) in an output cell?
I.e. something like the following but with syntax highlighting of the result:
with open('my_file.py', 'r') as f:
print(f.read())
I want the file content to be stored with the .ipynb file but I don't want it to be executed when I do Cell -> Run All.
Is there a command similar to %psource which shows the source code in an output cell instead of a pager?
Example code based on answer by #Matt:
from pygments import highlight
from pygments.lexers import PythonLexer
from pygments.formatters import HtmlFormatter
import IPython
with open('my_file.py') as f:
code = f.read()
formatter = HtmlFormatter()
IPython.display.HTML('<style type="text/css">{}</style>{}'.format(
formatter.get_style_defs('.highlight'),
highlight(code, PythonLexer(), formatter)))
No there is not way to do that with current magics, but it is pretty easy using pygments and returning IPython.display.HTML(...).
10 years later, and there's now a much simpler solution:
https://ipython.readthedocs.io/en/stable/api/generated/IPython.display.html#IPython.display.Code
from IPython.display import Code
Code(filename='my_file.py', language='python')