Data directory #11
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Data directory #11
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Draft: adding sequences functionality
Add function to create CSV file of sequences lookup
Minor changes post deployment
…lookup A bug in `create_sequences_lookup` meant that if any files were present in `<data_dir>/scanner_output/` then the function would attempt to find `that_file/sequences.csv` and include it in the combined `<data_dir>/sequences/all_sequences.csv` file. For example, it attempted to read in `scanner_output/some.rds/sequences.csv` which didn't exist.
Switch from selectize to native select.
UI selectors
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This pull request allows you (the developer, or whoever deploys the app) to declare a data-directory wherein the static-plots and data used within the app are stored.
By default the data-directory will coincide with the
./inst/app/data/directory within the package.If the environment variable "APP_DATA_DIR" is set, the app will use this to define the data-directory for the app.
Details of how to specify this environment variable are included in the README.
Any data-directory must contain the subdirectories
mutations,scanner_output,sequences,treeviewand have a structure identical to that in./inst/app/data/. (Once mrc-ide/tfpscanner#8 is merged into {tfpscanner}, this can be created usingtfpscanner::create_browser_data())Notes:
This has now been tested with the western-cape demo dataset.
Much of the work in this PR involved ensuring the data directory was declared in a single place, and that single definition used elsewhere in the app. Previously, paths to ./inst/app/www/data were hardcoded in many places.
The
update_data()function, and it's description in the README have been removed. The responsibility for setting up data directories that are of the correct structure for the app has been moved to tfpscanner.Note that the app cannot currently work with the datasets that are stored in ./inst/app/www/data. There are .rds files in there that contain ggplot2/ggtree objects that were generated a while ago. Attempts were made to find a version of ggtree/ggplot2 and/or their dependencies that allowed these files to be imported. This was very time-consuming and was ultimately a failure. These files could be regenerated using up-to-date packages if necessary.
2024-01-22
Changes to the UI have been incorporated into this branch. Details of the changes can be found in jumpingrivers#66
Briefly, these put all selectors into a collapsible sidebar, make all selectors into dropdown-type, and make the mutation/sequence selectors invisible except for when the current treeview admits highlighting mutations or sequences.