make_microreact_metadata_for_country.RdMakes a combined metadata table for a specified country.
make_microreact_metadata_for_country( country, species, user_email, list_of_countries_sheet_url = "https://docs.google.com/spreadsheets/d/13QlFTCJJXlNUp52bn6eM3eFhH_cM1DMTFo-VNwB4Q4U", sample_ids = NULL, reference = TRUE, present_colour = "#ff6b6b", absent_colour = "#efefef", max_number_genes = 5 )
| country | A string with the name of the country that matches that contained in the list_of_countries_sheet_url master sheet |
|---|---|
| species | A string for the species for which the microreact will be generated |
| user_email | A user email that has access to the master Google sheet (required) |
| list_of_countries_sheet_url | A string containin the master Google sheet which lists the sub sheet for each unit |
| sample_ids | A list of sample ids to be used within the micoreact. This will usually be generated from a tree e.g using the ape package tree <- ape::read.tree('path/to/newick/file') sample_ids <- tree$tip.label |
| reference | A boolean that determines if the sample_ids list contains a reference (assumes it is the id which does not match the pattern 'G[0-9]8') and should be added to the microreact metadata |
| present_colour | The colour to use in Microreact when a locus is present |
| absent_colour | The colour to use in Microreact when a locus is absent |
| max_number_genes | The maximum number of genes names in a column label before a common prefix is taken |
A microreact compatible dataframe for the specified country