Removing white spaces around plots in R Markdown / Quarto

R
R tips
Author

Philippe Massicotte

Published

August 15, 2022

When plotting spatial data, such as a geographical map, maintaining a proper aspect ratio is important. Whereas knitr::plot_crop() works fine to crop a file, how can we do the same operation for a figure inside an R Markdown or a Quarto document? Thanks to knitr, this can be done with a hook.

Close up on a grain field

Let’s crop something! Photo by Ant Rozetsky on Unsplash

I will use the polygon of Greenland to illustrate the issue.

greenland <-
  ne_countries(
    country = "greenland",
    returnclass = "sf",
    scale = "medium"
  )

# Find a proper projection
proj <- as.numeric(crsuggest::suggest_crs(greenland)$crs_code[1])
proj
#> [1] 5922

If we plot the map, we can see that there are white spaces around the image to keep the proper aspect ratio. This is not a problem per se, but one might be interested to fill up the ploting area with the actual plot.

```{r plot-original}
greenland |>
  ggplot() +
  geom_sf(size = 0.25) +
  coord_sf(crs = proj) +
  theme(
    plot.background = element_rect(fill = "#3c3c3c"),
    panel.border = element_rect(color = "red", fill = NA),
    panel.grid = element_blank(),
    panel.background = element_rect(fill = "#3c3c3c", color = "red"),
    axis.text = element_blank(),
    axis.ticks = element_blank()
  )
```

Now, I will create a hook named crop that is associated with the knitr::hook_pdfcrop() function.

```{r}
knitr::knit_hooks$set(crop = knitr::hook_pdfcrop)
```
Note

Note that the magick package and probably the underlying system library need to be installed on your system to crop images.

With that, we can use crop: true in a code chunk to call it and crop the displayed graph.

```{r plot-cropped}
#| crop: true
greenland |>
  ggplot() +
  geom_sf(size = 0.25) +
  coord_sf(crs = proj) +
  theme(
    plot.background = element_rect(fill = "#3c3c3c"),
    panel.border = element_rect(color = "red", fill = NA),
    panel.grid = element_blank(),
    panel.background = element_rect(fill = "#3c3c3c", color = "red"),
    axis.text = element_blank(),
    axis.ticks = element_blank()
  )
```

VoilΓ  πŸ‘, no more borders around the image.

Session info 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.0 (2024-04-24)
#>  os       Linux Mint 21.3
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language en_CA:en
#>  collate  en_CA.UTF-8
#>  ctype    en_CA.UTF-8
#>  tz       America/Montreal
#>  date     2024-05-03
#>  pandoc   2.9.2.1 @ /usr/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  ! package           * version date (UTC) lib source
#>  P base64enc           0.1-3   2015-07-28 [?] RSPM
#>  P cachem              1.0.8   2023-05-01 [?] RSPM
#>  P class               7.3-22  2023-05-03 [?] CRAN (R 4.3.1)
#>  P classInt            0.4-10  2023-09-05 [?] RSPM
#>  P cli                 3.6.2   2023-12-11 [?] RSPM
#>  P codetools           0.2-19  2023-02-01 [?] CRAN (R 4.2.2)
#>  P colorspace          2.1-0   2023-01-23 [?] RSPM
#>  P crosstalk           1.2.1   2023-11-23 [?] RSPM
#>  P crsuggest           0.4     2022-07-06 [?] RSPM
#>  P DBI                 1.2.2   2024-02-16 [?] RSPM
#>  P devtools            2.4.5   2022-10-11 [?] RSPM (R 4.4.0)
#>  P digest              0.6.35  2024-03-11 [?] RSPM
#>  P dplyr               1.1.4   2023-11-17 [?] RSPM
#>  P e1071               1.7-14  2023-12-06 [?] RSPM
#>  P ellipsis            0.3.2   2021-04-29 [?] RSPM
#>  P evaluate            0.23    2023-11-01 [?] RSPM
#>  P extrafont           0.19    2023-01-18 [?] RSPM
#>  P extrafontdb         1.0     2012-06-11 [?] RSPM
#>  P fansi               1.0.6   2023-12-08 [?] RSPM
#>  P farver              2.1.1   2022-07-06 [?] RSPM
#>  P fastmap             1.1.1   2023-02-24 [?] RSPM
#>  P fs                  1.6.4   2024-04-25 [?] CRAN (R 4.4.0)
#>  P generics            0.1.3   2022-07-05 [?] RSPM
#>  P ggplot2           * 3.5.1   2024-04-23 [?] RSPM
#>  P ggpmthemes        * 0.0.2   2024-04-25 [?] Github (pmassicotte/ggpmthemes@993d61e)
#>  P glue                1.7.0   2024-01-09 [?] RSPM
#>  P gtable              0.3.5   2024-04-22 [?] RSPM
#>  P htmltools           0.5.8.1 2024-04-04 [?] RSPM
#>  P htmlwidgets         1.6.4   2023-12-06 [?] RSPM
#>  P httpuv              1.6.15  2024-03-26 [?] RSPM
#>  P httr                1.4.7   2023-08-15 [?] RSPM
#>  P jsonlite            1.8.8   2023-12-04 [?] RSPM
#>  P KernSmooth          2.23-22 2023-07-10 [?] CRAN (R 4.3.1)
#>  P knitr               1.46    2024-04-06 [?] RSPM
#>  P later               1.3.2   2023-12-06 [?] RSPM
#>  P lattice             0.22-6  2024-03-20 [?] RSPM (R 4.4.0)
#>  P leafem              0.2.3   2023-09-17 [?] RSPM
#>  P leaflet             2.2.2   2024-03-26 [?] RSPM
#>  P lifecycle           1.0.4   2023-11-07 [?] RSPM
#>  P magick            * 2.8.3   2024-02-18 [?] RSPM
#>  P magrittr            2.0.3   2022-03-30 [?] RSPM
#>  P mapview             2.11.2  2023-10-13 [?] RSPM
#>  P memoise             2.0.1   2021-11-26 [?] RSPM
#>  P mime                0.12    2021-09-28 [?] RSPM
#>  P miniUI              0.1.1.1 2018-05-18 [?] RSPM (R 4.4.0)
#>  P munsell             0.5.1   2024-04-01 [?] RSPM
#>  P pillar              1.9.0   2023-03-22 [?] RSPM
#>  P pkgbuild            1.4.4   2024-03-17 [?] RSPM (R 4.4.0)
#>  P pkgconfig           2.0.3   2019-09-22 [?] RSPM
#>  P pkgload             1.3.4   2024-01-16 [?] RSPM (R 4.4.0)
#>  P png                 0.1-8   2022-11-29 [?] RSPM
#>  P processx            3.8.4   2024-03-16 [?] RSPM
#>  P profvis             0.3.8   2023-05-02 [?] RSPM (R 4.4.0)
#>  P promises            1.3.0   2024-04-05 [?] RSPM
#>  P proxy               0.4-27  2022-06-09 [?] RSPM
#>  P ps                  1.7.6   2024-01-18 [?] RSPM
#>  P purrr               1.0.2   2023-08-10 [?] RSPM
#>  P quarto            * 1.4     2024-03-06 [?] RSPM
#>  P R.cache             0.16.0  2022-07-21 [?] RSPM
#>  P R.methodsS3         1.8.2   2022-06-13 [?] RSPM
#>  P R.oo                1.26.0  2024-01-24 [?] RSPM
#>  P R.utils             2.12.3  2023-11-18 [?] RSPM
#>  P R6                  2.5.1   2021-08-19 [?] RSPM
#>  P raster              3.6-26  2023-10-14 [?] RSPM
#>  P Rcpp                1.0.12  2024-01-09 [?] RSPM
#>  P remotes             2.5.0   2024-03-17 [?] RSPM (R 4.4.0)
#>  P renv                1.0.7   2024-04-11 [?] RSPM (R 4.4.0)
#>  P rlang               1.1.3   2024-01-10 [?] RSPM
#>  P rmarkdown           2.26    2024-03-05 [?] RSPM
#>  P rnaturalearth     * 1.0.1   2023-12-15 [?] RSPM
#>  P rnaturalearthdata * 1.0.0   2024-02-09 [?] RSPM
#>  P rstudioapi          0.16.0  2024-03-24 [?] RSPM
#>  P Rttf2pt1            1.3.12  2023-01-22 [?] RSPM
#>  P satellite           1.0.5   2024-02-10 [?] RSPM
#>  P scales              1.3.0   2023-11-28 [?] RSPM
#>  P sessioninfo         1.2.2   2021-12-06 [?] RSPM (R 4.4.0)
#>  P sf                * 1.0-16  2024-03-24 [?] RSPM
#>  P shiny               1.8.1.1 2024-04-02 [?] RSPM (R 4.4.0)
#>  P sp                  2.1-4   2024-04-30 [?] CRAN (R 4.4.0)
#>  P stringi             1.8.3   2023-12-11 [?] RSPM
#>  P stringr             1.5.1   2023-11-14 [?] RSPM
#>  P styler            * 1.10.3  2024-04-07 [?] RSPM
#>  P terra               1.7-71  2024-01-31 [?] RSPM
#>  P tibble              3.2.1   2023-03-20 [?] RSPM
#>  P tidyselect          1.2.1   2024-03-11 [?] RSPM
#>  P tinytex             0.50    2024-03-16 [?] RSPM
#>  P units               0.8-5   2023-11-28 [?] RSPM
#>  P urlchecker          1.0.1   2021-11-30 [?] RSPM (R 4.4.0)
#>  P usethis             2.2.3   2024-02-19 [?] RSPM (R 4.4.0)
#>  P utf8                1.2.4   2023-10-22 [?] RSPM
#>  P vctrs               0.6.5   2023-12-01 [?] RSPM
#>  P withr               3.0.0   2024-01-16 [?] RSPM
#>  P xfun                0.43    2024-03-25 [?] RSPM
#>  P xtable              1.8-4   2019-04-21 [?] RSPM (R 4.4.0)
#>  P yaml                2.3.8   2023-12-11 [?] RSPM
#> 
#>  [1] /tmp/Rtmp84z1b8/renv-use-libpath-25ad1961f0a959
#>  [2] /tmp/Rtmp84z1b8/renv-sandbox
#> 
#>  P ── Loaded and on-disk path mismatch.
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────