At the end of a run, files found in the /results folder are collected and made available in the Reproduciblity pane, where users can view and download them. Files saved elsewhere will be discarded at the end of the run.

Results will be labeled Published Result in the Reproducibility pane:

Pereira et al. (2021) - SLEAP a deep learning system for multi-animal pose tracking Code Ocean 2022-02-15 at 5.08.04 PM

Why don't my graphics just show up?

Code Ocean has no built-in display. This is called headless execution, code executed this way is said to be run in batch mode. Plots, figures, and other graphics must be saved explicitly to the /results folder.

In MATLAB:

Use either print or saveas. The following snippet will save the same plot twice:

figure;
plot(1:10)
saveas(gcf, '../results/fig1.png')
print('../results/plot', '-dpdf')

In Python:

matplotlib is common for saving python graphics on Code Ocean.

Install matplotlib via a built-in package manager.
Set the backend to Agg first.

import matplotlib
matplotlib.use('Agg')
from matplotlib.pyplot import plot, savefig, figure
from numpy import linspace, pi, sin

x = linspace(0, 4 * pi)
y = sin(x)
fig = figure()
plot(x, y)
savefig('../results/plot.png')

In R:

In base R, you must call a graphics device:

Plot your graph
Save
ggplot2 has different syntax.

library(ggplot2)
## as png
png('../results/fig1.png')
g <- ggplot(mtcars, aes(x = wt, y = mpg)) + geom_point(); g
dev.off()

## as pdf
pdf('../results/fig1.pdf')
ggplot(mtcars, aes(x = wt, y = mpg)) + geom_point()
dev.off()

## ggsave
g <- ggplot(mtcars, aes(x = wt, y = mpg)) + geom_point()
ggsave('../results/fig1.tiff', g)

Linking or moving files to /results

If your code is already structured to save figures somewhere besides /results, use the Linux commands mv or ln -s.

To move figures currently saving to a folder called figures, write ln -s ../results ./figures in a shell script (typically called run.sh on Code Ocean) before you run your analyses.

If you are saving png files to the home directory, and if you have no png files there at the outset, write mv *.png ../result in a shell script. The * character is a wildcard and the command will apply to all files ending in.png.

You may also use Brace Expansion to move multiple types of files to /results, for example, mv *.{png,jpg,tiff} ../results .

Creating sub-directories within results

Each capsule begins with a shell script called run.sh . In this file, use the command mkdir -p to create sub-folders within /results. If you want to have all the figures in one subfolder and all the tables in another, at the end of the analysis, you would write something like:

mkdir -p ../results/figs && mv ../results/*.png ../results/figs
mkdir -p ../results/tables && mv ../results/*.txt ../results/tables

Alternatively, you can save the results of different analyses into different subfolders, as can be seen in the run.sh script of this capsule.