{tfpscanner}

Installation

remotes::install_github("mrc-ide/tfpscanner")

Use with {tfpbrowser}

{tfpscanner} is able to produce data that can be used in the {tfpbrowser} application. That app must be pointed to a data-directory that contains the tfpscanner-generated files (see the notes in {tfpbrowser} for details).

The structure of the data-directory used by tfpbrowser is as follows:

<data-root>
  |- mutations
  |  |- all_mutations.csv
  |  |- defining_mutations.csv
  |- scanner_output
  |  |- <clusterID1>
  |  |  |- cocirculating_lineages.csv
  |  |  |- lineage_composition.csv
  |  |  |- regional_composition.csv
  |  |  |- sequences.csv
  |  |  |- summary.csv
  |  |- <clusterID2>
  |  |  |- <as for clusterID1>
  |  |- ...
  |- sequences
  |  |- all_sequences.csv
  |- treeview
    |- node_lookup
    |  |- sina-logistic_growth_rate.csv
    |  |- tree-logistic_growth_rate.csv
    |  |- (a .csv for each .rds file in ./treeview)
    |- sina-logistic_growth_rate.rds
    |- tree-logistic_growth_rate.rds
    |- tree-mutations.rds
    |- tree-sequences.rds
    |- (various other .rds files containing trees that are presented by tfpbrowser)

The files in that data directory can be populated using tfpscanner::create_browser_data(). To run that function requires that a few files are in place:

• A directory into which the tfpbrowser files are to be added has been added to the file-system
• That data directory contains a scanner_output directory (this is typically generated by tfpscanner::tfpscan())
• A scanner environment file (typically having the name scanner_output/scanner-env-<date>.rds), as generated by tfpscanner::tfpscan() is present in the data-directory

Suppose:

• your data-directory was ./tfpbrowser_files/;
• the files generated by tfpscan() had been added to ./tfpbrowser_files/scanner_output/; and
• the scanner-environment file was ./tfpbrowser_files/scanner_output/scanner-env-2023-07-05.rds.

Then, to set up all the remaining files required by tfpbrowser, you would make the following function call:

tfpscanner::create_browser_files(
  e0 = "tfpbrowser_files/scanner_output/scanner-env-2023-07-05.rds",
  output_dir = "tfpbrowser_files",
  [any additional arguments to be passed on to `tfpscanner::treeview()`]
)