R package figur: Smart Handling of Figures, Tables and Code in RMarkdown Documents
You may fetch the package easily with devtools:
devtools::install_github('PiotrTymoszuk/figur')
For the full functionality with Rmakdown documents, please install also rmarkdown, knitr, bookdown and flextable. cowplot and patchwork are recommended as excellent tools to generate panels of multiple ggplot objects.
Handling ggplot figures
The core functionality of the figur package is the convenient storage and insertion/referencing of figures, preferably in the ggplot format, in RMarkdown documents. You may create ggplot graphs in an usual way:
library(tidyverse)
library(cowplot) ## to create multi-graph panels
## plotting data
test_cars <- mtcars %>%
rownames_to_column('car') %>%
as_tibble
> test_cars
# A tibble: 32 × 12
car mpg cyl disp hp drat wt qsec vs am gear carb
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 Mazda RX4 21 6 160 110 3.9 2.62 16.5 0 1 4 4
2 Mazda RX4 Wag 21 6 160 110 3.9 2.88 17.0 0 1 4 4
3 Datsun 710 22.8 4 108 93 3.85 2.32 18.6 1 1 4 1
4 Hornet 4 Drive 21.4 6 258 110 3.08 3.22 19.4 1 0 3 1
5 Hornet Sportabout 18.7 8 360 175 3.15 3.44 17.0 0 0 3 2
6 Valiant 18.1 6 225 105 2.76 3.46 20.2 1 0 3 1
7 Duster 360 14.3 8 360 245 3.21 3.57 15.8 0 0 3 4
8 Merc 240D 24.4 4 147. 62 3.69 3.19 20 1 0 4 2
9 Merc 230 22.8 4 141. 95 3.92 3.15 22.9 1 0 4 2
10 Merc 280 19.2 6 168. 123 3.92 3.44 18.3 1 0 4 4
# … with 22 more rows
# ℹ Use `print(n = ...)` to see more rows
## plots
car_dist <- test_cars %>%
ggplot(aes(x = mpg,
y = reorder(car, mpg))) +
geom_bar(stat = 'identity',
fill = 'steelblue') +
theme_classic() +
theme(axis.title.y = element_blank()) +
labs(title = 'Miles per gallon')
car_cyl <- test_cars %>%
ggplot(aes(x = cyl,
y = mpg,
color = factor(gear))) +
geom_point(shape = 16,
position = position_jitter(width = 0.1, height = 0.15)) +
theme_light() +
labs(title = 'Mlies per gallon',
fill = 'Gears')
car_panel <- plot_grid(car_dist,
car_cyl,
ncol = 2,
labels = LETTERS)
Subsequently, they can be converted into figure class objects keeping together the graph, its width and height (w and h), label representing the file name on the disc, reference name (ref_name) and caption used later in the RMarkdown document. This can be easily done by calling as_figure():
## call as_figure() to create a figure object
fig_list <- list(fig1 = as_figure(car_dist,
w = 90,
h = 90,
label = 'test1',
ref_name = 'test1_figure',
caption = 'caption for Figure 1'),
fig2 = as_figure(car_cyl,
w = 90,
h = 90,
label = 'test2',
ref_name = 'test2_figure',
caption = 'caption for Figure 2'))
car_figure <- as_figure(car_panel,
label = 'car_panel',
w = 180,
h = 120,
unit = 'mm')
The subsequent insertion of a figure chunk in the RMarkdown document works seamlessly with the insert() method. The dimensions are automatically converted into inches or provided as a function call. By default, the figure chunk is copied to your clipboard. Alternatively, it can append an existing .Rmd file.
Of note, the insert() method takes care for chunk names compatible with the standard Rmarkdown/bookdown format, e.g. by substitution of '_':
## canonical Rmarkdown/bookdown format: the chunk is copied into the clipboard
insert(fig_list$fig1)
# ```{r fig-test1-figure, fig.width = 3.543307083, fig.height = 3.543307083, fig.cap = 'caption for Figure 1'}
# fig_list$fig1$plot
# ```
# __Figure \@ref(fig:fig-test1-figure). caption for Figure 1__
# _<<legend>>_
## dimensions as a functon call: insensitive to later resizing of the figure
insert(fig_list$fig2, relative_dim = TRUE)
# ```{r fig-test2-figure, fig.width = figur::convert(fig_list$fig2, to = 'in')$w, fig.height = figur::convert(fig_list$fig2, to = 'in')$h, fig.cap = 'caption # for Figure 2'}
# fig_list$fig2$plot
# ```
# __Figure \@ref(fig:fig-test2-figure). caption for Figure 2__
# _<<legend>>_
Finally, by calling refer() a Rmarkdown/bookdown-compatible reference to the figure is generated and, by default, copied to the clipboard. To save the figure on the disc, use pickle() - the file name and image dimensions are stored in the object:
## referencing
refer(fig_list$fig1)
Figure \@ref(fig:fig-test1-figure)
pickle(fig_list$fig1)
Handling data frames
Basically, any data frame may be converted to an mdtable object, which as in case of graph-storing figur instance, bundles the data frame with its later reference and caption in the Rmarkdown document:
test_tbl <- as_mdtable(mtcars,
label = 'mt_cars',
ref_name = 'mt_cars',
caption = 'Car data')
> head(test_tbl)
mpg cyl disp hp drat wt qsec vs am gear carb
Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4
Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4
Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1
Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1
Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2
Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1
Insertion of the corresponding chunk into the Rmarkdown document and referencing is analogically done with the insert() and refer() methods. By default, the output is copied to the clipboard:
> insert(test_tbl)
# ```{r tab-mt-cars, tab.cap = 'Car data'}
# flextable::flextable(test_tbl)
# ```
> refer(test_tbl)
Table \@ref(tab:tab-mt-cars)
Handling R code
Management of R code in Rmarkdown may pose a challenge, especially in lengthy documents with multiple repeating inline code elements. Additionally, debugging may consume lots of time. A smarter alternative to the 'copy-paste' approach and tesing the code in the console is provided with the mdexpr object. Virtually any R expression may be wrapped with mdexpr() which stores the text code representation and evaluation result. By this means, any evaluation errors are directly reported:
## error-free evaluation
test_mdexpr <- mdexpr(nrow(mtcars), ref_name = 'mtcar_size')
> test_mdexpr
mdexpr: {nrow(mtcars)} = 32
## errors are raised at creation of the mdexpr:
> mdexpr(mtcars$mpg[1, 2], ref_name = 'mtcar_size')
Error in mtcars$mpg[1, 2] : incorrect number of dimensions
The code chunk is inserted as an inline element with the refer() call and as a multi-line chunk with the insert() method. By default, the output is copied into the clipboard:
> refer(test_mdexpr)
# `r nrow(mtcars)`
> insert(test_mdexpr)
#```{r mtcar-size}
#nrow(mtcars)
#```
Bibliography
In my experience, a combination of an external citation manager and R Studio is not the most efficient one. The mdbib object storing the bibliography derived from the most common BibTex format and enabling for search via regular expression and referencing directly from R can make management of literature references more straightforward.
To create a mdbib object, just read your BibTex file from the disc with read_bib():
mol_bib <- read_bib('./test/mol_biblio.bib')
> mol_bib
# A tibble: 10 × 33
CATEGORY BIBTEXKEY ADDRESS ANNOTE AUTHOR BOOKT…¹ CHAPTER CROSS…² EDITION EDITOR HOWPU…³ INSTI…⁴ JOURNAL KEY MONTH NOTE NUMBER
* <chr> <chr> <chr> <chr> <list> <chr> <chr> <chr> <chr> <list> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 ARTICLE Cavalier… NA NA <chr> NA NA NA NA <chr> NA NA JCO pr… NA nov NA 5
2 ARTICLE Wu2020 NA NA <chr> NA NA NA NA <chr> NA NA Molecu… NA jun NA 1
3 ARTICLE Ding2022 NA NA <chr> NA NA NA NA <chr> NA NA Fronti… NA feb NA NA
4 ARTICLE Wichmann… NA NA <chr> NA NA NA NA <chr> NA NA Intern… NA dec NA 12
5 ARTICLE Keck2015 NA NA <chr> NA NA NA NA <chr> NA NA Clinic… NA feb NA 4
6 ARTICLE Walter20… NA NA <chr> NA NA NA NA <chr> NA NA PloS o… NA feb NA 2
7 ARTICLE VanHooff… NA NA <chr> NA NA NA NA <chr> NA NA Journa… NA nov NA 33
8 ARTICLE Lawrence… NA NA <chr> NA NA NA NA <chr> NA NA Nature… NA jan NA 7536
9 ARTICLE Mermel20… NA NA <chr> NA NA NA NA <chr> NA NA Genome… NA apr NA 4
10 ARTICLE Benjamin… NA NA <chr> NA NA NA NA <chr> NA NA bioRxiv NA dec NA NA
# … with 16 more variables: ORGANIZATION <chr>, PAGES <chr>, PUBLISHER <chr>, SCHOOL <chr>, SERIES <chr>, TITLE <chr>, TYPE <chr>,
# VOLUME <chr>, YEAR <dbl>, ABSTRACT <chr>, DOI <chr>, ISSN <chr>, KEYWORDS <chr>, MENDELEY.TAGS <chr>, PMID <chr>, URL <chr>,
# and abbreviated variable names ¹BOOKTITLE, ²CROSSREF, ³HOWPUBLISHED, ⁴INSTITUTION
# ℹ Use `colnames()` to see all variable names
Technically, the mdbib instance is nothing else as a data frame or tibble which may be searched with your favourite tool set like tidyverse's filter().
The figur package offers also a possibilty to search with regular expressions via reglook(). Finally, the citations can be easily pasted into your Rmarkdown document by calling refer(). The whole procedure works particularly caompact in a pipeline:
## be default the output is copied into the clipboard:
mol_bib %>%
reglook(regex = '(The Cancer)|(GSE\\d+)') %>%
refer
# [@Cavalieri2021; @Lawrence2015]
The package is available under a GPL-3 license.
The package maintainer is Piotr Tymoszuk.
figur uses tools provided by the rlang, tidyverse, stringi, flextable, knitr, clipr and bib2df.