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feat: export an R script that reproduces the app - #149
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The Export page shows and downloads an R script that repeats the analysis of the app: load_rcc() with the settings of the object, or the example data, then normalise() with the method, background and thresholds chosen in the app. The thresholds are written into the script and read back with read_thresholds(), so it is one file.
The thresholds come from thresholds_yaml(), which write_thresholds() now uses too, and the example data is recognised from a cached fingerprint of its load time and samples, which normalise() leaves alone.
An unknown instrument is left to load_rcc(), the folder the object was loaded from is kept unless it was an upload, and the script says that it loads every file of the folder.
…he script The R script for an upload says which columns the sample sheet needs, and its tests no longer depend on where they run.
An object reopened in a later session can hold a folder that no longer exists, so the script asks for the path instead.
mcanouil
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Type: Enhancement 💡
mcanouil
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October 15, 2026 13:51
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The Export page now has a "Reproduce in R" card.
It shows an R script that repeats the analysis of the app, and downloads it as
nacho-reproduce.R.The script loads the data with
load_rcc()and the settings stored in the object, then callsnormalise()with the method, background and number of RUVg factors chosen in the app.The thresholds set in the app are written into the script as YAML and read back with
read_thresholds(), so the script is a single file.For the example data, it starts from
GSE74821and runs as it is.For other data, it keeps the folder the object was loaded from, or asks for the paths when the files were uploaded or the folder is gone, and names the sample sheet columns.
The tests run the generated script and check that it gives the same counts, quality-control table and thresholds as the app.
write_thresholds()now builds its text with a new internalthresholds_yaml(), which the script uses too.