Hands-off running: Automatically saving figures#

Say you have 53 figures and 23 tables, the latter created from 161 different specifications. That makes for a lot of work when re-running the code, if you haven’t automated the saving of said figures and tables.

Warning

We have seen instructions that tell the replicator to right-click and save the figures. While there is no substitute for comparing all these figures, that’s too much work!

TL;DR#

  • Save all figures using commands, rather than manually.

  • It’s easy.

Saving figures programmatically#

In order to be able to enable “hands-off running”, saving figures (and tables) automatically is important. I will show here a few simple examples for various statistical programming languages.

After having created the graph (”graph twoway”, “graph bar”, etc.), simply add “graph export "name_of_file.graph-extension", replace”. Many formats are available, as required by journal requirements.

sysuse auto
graph twoway (lfitci mpg disp) (scatter mpg disp)
graph export "path/to/figure1.png"

For more information, see https://www.stata.com/manuals/g-2graphexport.pdf.

Methods vary, but the two main ones are redefining the graphics device for the desired format, or using the ggsave wrapper. Examples for both, below.

attach(mtcars)
fit <- lm(mpg ~ disp)
png(filename=file.path("path","to","figure1.png"))
plot(fit)
dev.off()

(for more information, see help pages for “?png”, “?eps”, or “?pdf”)

library(ggplot2)
library(here)
figures <- here::here("figures")

ggp <- ggplot(mtcars,aes(mpg,disp)) + 
       geom_point()+ 
       stat_smooth(method = "lm",geom="smooth" )
ggsave(ggp,file.path(figures,"figure1.png"))

(for more information, see https://ggplot2.tidyverse.org/reference/ggsave.html)

There are many ways to do this in Python, which is often geared towards “head-less” processing. Even if using Jupyter notebooks, you should save the figures!

import matplotlib.pyplot as plt
import os

plt.plot([1, 2, 3], [1, 4, 9])
plt.show()
plt.savefig(os.path.join("figures",'foo.png'))
plt.savefig(os.path.join("figures",'foo.pdf'))

bar(x);
saveas(gcf,fullfile('path','to','figure1.png'))

Takeaways#

What this does#

This ensures

  • that your code runs without problem, after all the debugging.

  • that your code runs without manual intervention.

  • that you do not impose fallible and onerous work on replicators

What this does not do#

This does not ensure

  • that your code generates a log file that you can inspect, and that you could share with others.

  • that it will run on somebody else’s computer

    • because it does not guarantee that all the software is there

    • because it does not guarantee that all the directories for input or output are there

    • because many intermediate files might be present that are not in the replication package

    • because it does not guarantee that all the directory names are correctly adjusted everywhere in your code

  • that it actually produces all the outputs

    • because some outputs might be present from test runs

What to do next#

To solve some of these problems, let’s go to the next step.