A tool for reproducible research: From data analysis (in R) to a typeset laboratory notebook (as .pdf) using the text editor Emacs with the 'mp' package

Motivation

One of the primary goals of any experimental research is to produce a nicely typeset document which explains the methods and results. This should be sufficient to allow the reader to recreate the work and thus to verify the results (given the correct tools).

In practice, much research is documented by adapting existing 'office'-type software for this purpose (Microsoft, OpenOffice etc.).

While there is much to be said for the ease of use of these techniques, they are not ideally suited to the purpose. In particular, those that employ a 'point-and-click' graphical user interface (GUI) make it impossible to recreate these steps (mouse movements and clicks). The options for generating graphs and analysing data are typically limited and often require the use of separate 'third-party' software for these steps (e.g. SPSS, GraphPad Prism). This again makes the reproduction of results a challenge.

There are many free and open source alternatives which are designed with the needs of the laboratory researcher in mind. Ease of use appears to be the principle reason for their lack of widespread use. The mp (for 'make-pdf') package came about as an attempt to bring elements from a number of these diverse sources together. Data analysis is performed using R¹. Typesetting is performed using LaTeX, which has become the industry standard for scientific publications^2,3. mp was also motivated by the repetitive nature of much laboratory research. Successive experiments often differ little in method and the analysis often uses the same techniques with new data each time.

Emacs is the text editor which brings these methods together. Emacs itself has been criticized for lack of ease of use, although if used purely as a text/file editor, as in the examples here, it remains quite simple⁴.

The examples do require some familiarity with R. The transition from familiar GUI-style data-analysis to terminal-based output may also appear daunting at first. For those considering taking the plunge we hope that these simple examples will help to illustrate how easy the language can be to use. As a long-term investment, we feel that the time taken to become familiar with these methods is likely to be more than compensated by subsequent improvements in the speed and simplicity of work-flow.

What does mp do

mp is a collection of functions and variables which makes and displays a .pdf from 'the materials available'. It aims to do so 'at the touch of a button'. It works primarily with the following file types:

The final .pdf is generated with latexmk⁵. mp supports the use of indexes, glossaries, nomenclatures and bibliographies (e.g. with a separate .bib file)^6–8.

The output from the whole process is shown in a new window; once complete, errors, warnings and success are highlighted; this typically makes correcting errors more straightforward. Once the .pdf has been generated, it is opened with a viewer (by default 'evince'⁹).

The red arrow in Figure 1 shows the default route taken through these file types. The function mp-mp can be called on any of the file types above, or on a directory containing such files. Thus it may be used solely, for example, in converting .tex to .pdf.

Figure 1. Flow diagram showing file types and converters in the mp package.

The red arrow shows the default flow path.

When the process is repeated, prior files are as over-written. Thankfully, Emacs will, by default, save files automatically when modified, although clearly caution is still required.

The most important variable is the intermediary (or 'go-between') file and the step which follows. This intermediary is either a no-web (.Rnw) or an .org file^10,11.

.R files. Typically, it is easier to perform data analysis using an .R file directly vs. a more cumbersome intermediary .Rnw or .org.

The .R file is broken up into 'chunks' of code, which (by default) correspond to sections in a corresponding LaTeX document (to be generated). These are separated by headers: ## ---- chunkName. This follows the convention introduced by knitr for naming chunks.

No other 'markup' is employed when processing the .R file. If .org is used as the intermediary, there is an option to convert LaTeX math mode in the .R comments to inline math in LaTeX (as shown later in example 4).

A typical use case would thus involve writing R code (in a .R file), using mp to generate an 'intermediary' .Rnw file then 'fleshing out' the latter to include additional explanatory text:

.Rnw files. Another approach is to write the .Rnw file directly. R code can be integrated into the document; alternatively, an .R file with the same name may be used for the code chunks; mp will try to match the chunks in that file to the sections in the .Rnw document. New sections are added, as necessary, while preserving the a common order between the documents where possible.

Entwiners

The intermediary file is then passed on to one of the tools below. Following the existing trend to name these instruments after processes involved in fabric making, we refer to them collectively as 'entwiners'.

mp uses templates (particularly for the preamble) when generating intermediary files; there is one for each entwiner. These contain defaults that are based on the authors' own work-flow. For example, the LaTeX package siunitx is included to allow for the correct display of scientific units¹². Our 'hello world' example (Listing 2 below), while too simple to make use of the additional packages loaded, does show how multiple options are set in LaTeX and R (including knitr).

.el files. mp can also generate documentation for an elisp package which is contained in one file. This is done using .org as the intermediary. This feature was added to emulate the nicely typeset package documentation that is standard in R and LaTeX. As an example, the manual for the mp package itself was generated this way and is given as supplementary material.

Control flow

A more detailed diagram, which also shows the customizable variables, is available as Supplementary material (mpFlow.pdf). Some familiarity with setting 'customizable variables' is required when moving beyond the default settings for mp. For more experienced users, knowledge of these functions and variables allows for highly granular control, if desired.

Why elisp?

mp depends on an array of tools. Some are command-line, some use R and some are Emacs packages^5,11,13–15. We settled on elisp, the native language of Emacs as it allows for easy integration of these diverse methods 'under one roof'¹⁶. There is a good deal of 'text manipulation' involved; as an extensible text-editor, Emacs is particularly well suited to this task.

Elisp supports asynchronous processing. That is, the Emacs terminal is not 'frozen' during the process of .pdf generation and thus an R session or text editing can continue uninterrupted.

Lisp itself, while no longer popular, is arguably comparable in efficiency and speed to any of the widely used programming languages. It can be interpreted, allowing for rapid development; and compiled, allowing for improvements in speed when required. While the syntax if often said to be 'off-putting' initially, it may also be described as 'expressive', allowing for the concise and efficient representation of problems. Any language with the ability to write to and read from files and send text to the command line could have been used for the purpose. Thus the methods could have been implemented in R or LaTeX, although perhaps in a more lengthy and less readable form. Doing so would also lose some of the tight integration with Emacs which was a goal of the package.

Related tools

Methods used by mp

Converting from an intermediary to a .tex file is performed by one of the entwiners shown in Table 1.

Sweave. This is the oldest and best-supported of these converters¹³. It is the only such method supported by R-core. It continues to be used as a standard tool for R package developers writing vignettes.

It does suffer from a number of limitations relative to its counterparts. In particular, the displayed code 'as-is' has little formatting and no color. Only one figure per 'chunk' is supported. This may be overcome by reading/writing files in R directly, although this can be tricky to implement.

Knitr. This has superseded Sweave for most practical purposes¹⁴. The code is much easier to read. It also allows for multiple figures per chunk, with their own captions. It allows the chunks to be kept in a separate source file - as opposed to requiring them to be part of the .Rnw file. There are more options for the display of terminal output, including handling of error messages. Like Sweave, it can be used to build R package vignettes.

org-mode. .org files are arguably more intuitive to read and edit than .tex, particularly for users new to the latter. Tables are simpler to read, create and modify. The use of 'collapsible' section headers makes it easy to see the structure of a document at-a-glance before expanding one section for further editing^17,18.

While org-mode loses the attractive code printing of knitr, some worthy alternatives are provided by the LaTeX package listings¹⁹. In mp, the default settings adopted for listings are modeled after the knitr defaults (although admittedly not quite as attractive).

These include the option to include LaTeX maths markup in the code commentary, for example to display equations.

Like Sweave, org-mode chunks suffer from the drawback that multiple figures per chunk are not supported by default.

By contrast with the other entwiners, Org-mode allows for conversion/export to multiple file types. By default, mp converts .org to .tex but alternatives are straightforward, such as to .html or to .MARKDOWN.

Allied approaches

Converting .org to .Rnw is possible using the ravel package for Emacs²⁰. This is also possible with the pander package for R, which integrates R with the Haskell library pandoc^21,22. It is broader in scope than ravel and aims to convert a wide range of file types. Both could serve as alternatives to any of the entwiners above or be used in conjunction with them. We have chosen to stick with the three above as these appear better established.

Closer integration between R and LaTeX is possible using the LaTeX packages knitrl and spaper; although not yet part of the Comprehensive TeX Archive Network (CTAN), they are readily available on github^23,24. The author, Dr F Harrell, also provides some very useful .Rnw templates for use in statistical reporting; we encourage the reader to explore these methods at https://github.com/harrelfe/rlatex. mp, by contrast, takes the approach of storing its templates as customizable variables within Emacs. This has the potential advantage of having them 'close to hand' when working in Emacs, easy customization, type-checking and persistence across Emacs sessions.

Alternatives to mp

There are many other good tools available which aim to bridge the gap between .R and .pdf, although to our knowledge, mp is the one which allows the user to generate one file type from the other with a single keystroke. We suggest that having more options available for the task is by no means a bad thing; doubtless some of these methods will be more appealing depending on the users background or the task at hand.

RStudio. This integrated development environment (IDE) is the leading alternative to Emacs for working with R and generating .pdfs²⁵. It is probably the best choice for those new to combining R and LaTeX. It has a 'friendlier' GUI than Emacs and the menus arguably simplify access to functions. It has better integration with Rmarkdown (see below)²⁶. XeLaTeX is supported, although at the time of writing LuaLaTeX does not appear to be (in contrast to mp).

Having used RStudio on a daily basis for two years, our first author ultimately found Emacs to be preferable, primarily on account of the gain in speed when editing text/code and also due to the ability to customize and improve the environment as required for specific tasks. With RStudio, there is also the major drawback when compiling .pdfs that the application pauses with no output until the process is complete. It is also typically more 'memory hungry' than Emacs. If running multiple R sessions, a new copy of the application needs to opened for each. These limitations are minor for small files and data sets but can become a major inconvenience with more complex tasks. Finally, RStudio requires a license for commercial use, whereas all the elements in mp are freely available.

Rmarkdown. This R package is another way of feeding text and code to knitr. It combines the attractive features of the latter with a simplicity of style similar to org-mode. It too allows for export to multiple file types, including .html and Microsoft .doc. The process generates an additional .md file which is then processed by pandoc. Due to the additional dependencies introduced, we have not sought to include these methods in mp.

knitr. This entwiner already integrates with some GUI-style .tex editors, particularly LyX. The latter is part of 'Scientific Workplace' (SW), which, like mp, tries to make life easier for the laboratory researcher by providing a simplified work space. In the case of SW, a GUI is preferred to directly editing files²⁷.

Minted. This is an alternative to the listings package for typesetting code with LaTeX²⁸. While admittedly often more attractive for code display, it requires an external python dependency. Also, for code chunks which span more than one page, automating background coloring is currently challenging.

Experimental work: BHB, cell growth and migration

Beta-hydroxybutyrate is a source of energy produced by the liver when the body is in ketosis, i.e. when the availability of glucose/sugars as a source of fuel is limited.

Increasing ketones in the blood lead to higher rates of fatty acid oxidation and an increase in the production of acetyl-CoA. When the amount of acetyl-CoA exceeds the capacity of the tricarboxylic acid cycle to utilize it, there is an increase in the production of the ketone bodies (BHB and acetoacetate (AcAc)).

One of the hallmarks of cancer is the dysregulation of metabolism. Cancer cells are particularly dependent on glucose as an energy source whereas normal tissue can readily adapt to using ketone bodies as an alternative. This is in part due to genetic and mitochondrial defects in cancer cells^29–35.

Thus, a number of treatments involving the modification of diet to stimulate ketone production have been suggested: the ketogenic diet, caloric restriction and intermittent fasting. These strategies have been studied in various in vivo models of glioma, a malignant brain tumor. They have demonstrated increased survival as well as anti-tumor effects³⁶.

The ability of BHB to inhibit cancer cell growth and migration has long been recognized^37–39. The work from Magee et al., from 1979, also features the B16 melanoma cell line. These investigators demonstrated a reduction in the number of lung metastases following an injection of cells to the tail vein of mice, in those receiving a diet of just fats and water vs. sucrose and water.

This phenomenon is of particular interest to our laboratory as we have demonstrated that the ketogenic diet (whereby energy requirements are met almost exclusively with fat) enhances the response of glioma to radiation and chemotherapy in a mouse model⁴⁰.

We sought to determine whether the same phenomenon would be observed with other cancer types which are commonly metastatic to the brain; in particular melanoma.

Software implementation

The software may be obtained via e.g. git clone https://www.github.com/dardisco/mp

The following should then be placed in your init.el file:

(add-to-list 'load-path " /path/to/mp")
(require 'mp)

mp should then be available once Emacs starts. It is a 'minor mode' for Emacs; the sole keybinding invokes the function mp-mp with Ctrl-Alt-|(usually found above the 'Return' key; in Emacs parlance this is also known as C-M-|). mp-mp is a gateway to all of the package functions; these can also be run individually/'interactively' as required (using execute-extended-command).

mp-mp prompts for a file name; if none is supplied, it will look first at the current buffer. If this is not an .R, .Rnw, .org .tex or .el file it will select the appropriate file from the default-directory as that which has most recently modified. Thereafter it will search up the directory tree if no such file is found.

Instead of a file name, the single character 'p' may be given to display the appropriate .pdf associated with the current file or directory.

Operation

System requirements: this should work with any recent version of Emacs, which is platform independent (i.e. works on Windows, Linux, Mac-OS). Version ≥ 24.4 is recommended to allow for automated export of .org to .tex.

To export to HTML, the elisp package htmlize is required¹⁵.

A recent installation of R (>3.0) and TeX (2013 and on) is also assumed. We used TeX Live 2013 for these examples.

No support for caching is provided, although with short documents similar in scale to the examples below this should not result in much loss of performance. The time to compile is <10 secs with an Intel i5-2430M processor for all of the examples given. When speed is an issue, we suggest temporarily changing your PATH to allow the relevant R and LaTeX binaries to run from a temporary RAM drive.

'Hello world' with mp. We begin with the simplest use case. We create the directory hello and place the contents of Listing 1 into hello.R.

Listing 1: The file hello.R

## ---- Print hello
print(”Hello world”)
## ---- Here are two graphs
## here’s a comment
plot(1:10, 10:100)
## this second graph should appear
## below the first
plot(1:10, sqrt(1:10))

The final product, hello.pdf is shown in Figure 2.

Figure 2. The file hello.pdf.

The intermediary file hello.Rnw will be left open in Emacs for further modification and this is shown in Listing 2.

Listing 2: The file hello.Rnw

%
\documentclass{article}
%
% modified from default setup for knitr
%
\usepackage[]{graphicx}
\usepackage[]{color}
\usepackage{framed}
% recommended with ‘knitr’
\usepackage{alltt}
\usepackage{mathtools}
\usepackage[sc]{mathpazo}
\usepackage{geometry}
\geometry{verbose, tmargin=2.5cm, bmargin
    =2.5cm,
  lmargin=2.5cm, rmargin=2.5cm}
\setcounter{secnumdepth}{2}
\setcounter{tocdepth}{2}
\usepackage{url}
\usepackage{hyperref}
\hypersetup{unicode=true, pdfusetitle}
\hypersetup{bookmarks=true,
    bookmarksnumbered=true}
\hypersetup{bookmarksopen=true,
    bookmarksopenlevel=2}
\hypersetup{breaklinks=false, pdfborder={0 0
     1}}
\hypersetup{backref=false}
\hypersetup{colorlinks=true}
\definecolor{myDarkBlue}{rgb}{0, 0, 0.5}
\hypersetup{linkcolor=myDarkBlue}
\hypersetup{pdfstartview={XYZ null null 1}}
%
% Palatino family
\usepackage[T1]{fontenc}
\usepackage{mathpazo}
\linespread{1.05}
\usepackage[scaled]{helvet}
%
% other useful additions
%
%% for rerunfilecheck:
% no need to rerun to get outlines right
\usepackage{bookmark}
%% for nice tables
\usepackage{booktabs}
%% for e.g. \formatdate
\usepackage{datetime}
%% for SI units
\usepackage{siunitx}
%% for chemical symbols
\usepackage[version=3]{mhchem}
%% to use forced ’here’
%% e.g. \begin{figure}[H]
\usepackage{float}
%% for large numbers of floats
\usepackage{morefloats}
%% to keep floats in same section
\usepackage[section]{placeins}
%% for tables > 1 page
\usepackage{longtable}
%
%%----------------------------------------
%
\begin{document}
%
% knitr chunks
<<setup, include=FALSE>>=
library(knitr)
### Set global chunk options
opts_chunk$set(
eval=TRUE,
## text results
echo=TRUE,
results=c(’markup’, ’asis’, ’hold’, ’hide’)
    [1],
collapse=FALSE,
warning=TRUE, message=TRUE, error=TRUE,
split=FALSE, include=TRUE, strip.white=TRUE,
## code decoration
tidy=FALSE, prompt=FALSE, comment=’##’,
highlight=TRUE, size=’normalsize’,
background=c(’#F7F7F7’, colors()[479], c
    (0.1, 0.2, 0.3))[1],
## cache
cache=FALSE,
## plots
fig.path=c(’figure’, ’figure/minimal-’),
fig.keep=c(’high’, ’none’, ’all’, ’first’, ’
    last’)[1],
fig.align=c(’center’, ’left’, ’right’, ’
    default’)[1],
fig.show=c(’hold’, ’asis’, ’animate’, ’
    hide’)[1],
dev=c(’pdf’, ’png’, ’tikz’)[1],
fig.width=7, fig.height=7, #inches
fig.env=c(’figure’, ’marginfigure’)[1],
fig.pos=c(’’, ’h’, ’t’, ’b’, ’p’, ’H’)[1])
### Set R options
options(formatR.arrow=TRUE, width=60)
knit_hooks$set(inline = function(x) {
   ## if (is.numeric(x)) return(knitr:::format
       _sci(x, ’latex’))
  highr::hi_latex(x)
})
## uncomment below to change theme
## knit_theme$get()
## opts_knit$set(out.format=’latex’)
## thm1 <- knit_theme$get(’acid’)
## knit_theme$set(thm1)
@
% knitr read chunks
<<readChunks, include=FALSE>>=
read_chunk(’hello.R’)
@
\title{hello}
\author{Chris Dardis}

\maketitle
% page numbers appear top-right
\pagestyle{headings}
\tableofcontents

\subsection{Print hello}

<<Print hello>>=
@

\subsection{Here are two graphs}

<<Here are two graphs>>=
@

%
%% \bibliographystyle{plain}
%% \bibliography{hello}
 \end{document}

Experimental work

The purpose of the current work was to demonstrate an inhibitory effect of BHB on the growth and migration of a melanoma cell line in vitro. Details of the aims, methods, results and conclusions are given for each experiment separately as Supplementary material (see Table 2).

These experiments would normally make up just one part of an article, where it would be reasonable to combine all of these as one supplement. We provide the experiments separately for the sake of illustrating features of the mp package.

Cells. Melanoma B-16 cells were obtained from American Type Culture Collection (ATCC). To facilitate quantitative measurement of tumor growth, they were modified as described previously⁴¹. The cells were stably transfected with the gene encoding luc2 (luciferase) using the pGL4.51 [luc2/CMV/Neo] vector (Promega Corp, Madison, WI) and FuGENEH 6 Transfection Reagent (Roche Applied Science, Indianapolis, IN) following conditions specified by the manufacturer. They were then injected into the right ventricle of a mouse. These animals were sacrificed when bioluminescence was detected in the brain. Cells metastatic to the brain were recovered put into culture. These cells are designated B16-F1-Luc2-BR2.

Effects of BHB on growth. Firstly, it was necessary to determine the optimal starting number of cells to seed a growth curve. If the cells are plated too sparsely, they have a tendency not to grow. Likewise if the concentration is too great to start with, then this will make any difference due to the effect of BHB difficult to see. This is complicated further by growing the cells in a circular well - the cells are in closer communication close to the center and more separated close to the edge. One technical report suggested a starting number of 4000 per well in a 12-well plate for most cell lines⁴². In choosing a starting number, we were guided primarily by prior work in our own laboratory.

To determine whether BHB would inhibit cell growth, we chose a concentration of 10 mmol/L, again based primarily on our prior experience. Under normal conditions, serum BHB has an upper reference limit of 0.3–0.5 mmol/L. Tests of BHB concentration (for patients) are available commercially and are commonly used to aid in the diagnosis of diabetic ketoacidosis, where levels are usually at least 2 mmol/L.

Even higher levels are seen in patients adhering to the ketogenic diet. This diet is most commonly employed in the treatment of drug-resistant epilepsy, where serum BHB concentration has been shown to correlate with the degree of seizure control⁴³. In this study of 74 children, median levels were 8–10 mmol/L.

We chose a concentration of 10 mmol/L in order to be certain that an effect was present, before considering whether lower levels would be similarly efficacious.

Effects of BHB on migration. The scratch assay is a simple and widely used test to assess cell migration. Details of a typical protocol for the technique are available⁴⁴. Using the same cell line, we sought to illustrate impaired migration in the presence of BHB.

Software

The above examples illustrate some of the options available when using mp. While it may not be the tool of choice for every application, it has been a valuable addition to our own laboratory work and we hope this to be the case for others engaged in similar work.

Much scientific research is reported in the form of a summary and it has not been traditional for researchers to provide detailed accounts of the original experiments along with the original observations/results made at the time. We acknowledge that the details of individual experiments, particularly 'pilot' studies of an exploratory nature or those which yielded negative results are likely to be of limited interest to a general readership. Including these as supplements appears a reasonable approach.

The classic quote on reproducible research is from Buckheit and Donoho⁴⁷:

The same may well be said of biology. Within a traditional print-form journal, this is justifiable as constraints of space naturally limit the length of articles. However, this has been obviated by the option to refer to online-only Supplementary material.

Such resources may be valuable for those seeking to reproduce particular steps in the research. They may also may be of interest to those working on closely related problems, in particular by saving time on preparatory work. Providing original 'raw' data may also allow results to be combined with subsequent experiments. Furthermore, novel techniques, perhaps not developed at the time of writing, may later be applied by other researchers, perhaps leading to new or deeper insights.

Experimental work

The inhibitory effects of BHB on the growth of neoplastic cells has now been observed in a number of cells lines in our laboratory, as well as those of other investigators³⁷.

Impairment of growth of neoplastic cells due to ketones has been suggested to be in part due to the polyacetylation of histones⁴⁸. Ketone bodies also impair glycolysis, on which neoplastic cells are more heavily dependent. This occurs in part through inhibition of the activity of phosphofructokinase and hexokinase^49,50.

The finding that inhibition of growth occurs in a cell line selected for their propensity to metastasize to the brain is novel. Brain metastases are a significant contributor to morbidity and mortality in patients with cancer⁵¹. We feel that this approach deserves further investigation. In particular, it would be of interest to determine whether the same phenomenon would be observed in breast and lung cancer cell lines with a propensity to metastasize to the brain. It would also be interesting to determine whether the inhibitory effects of BHB on cancer cells are evident in vivo when ketones are given as a dietary supplement with a relatively normal diet - as opposed to the ketogenic diet, which may be challenging to adopt for patients affected by cancer.

Software

The mp package appears to be a useful addition to the tools available for facilitating reproducible research. Future development will likely include increased support for the LaTeX biblatex package. Collaboration and suggestions for improvement are welcome. Please try to address these to the development site on github if possible.

Experimental work

We have demonstrated here that BHB is inhibitory to the growth and migration of B16 B16-F1-Luc2-BR2 melanoma cells, which were selected for their propensity to form brain metastases, at a concentration of 10 mmol/L.

Source code

https://www.github.com/dardisco/mp

Archived source code as at the time of publication

http://dx.doi.org/10.5281/zenodo.21183⁴⁵

Software license

GPL >= 3