make_microreact_metadata.RdMakes a microreact compatible dataframe combining epi_data, ast_data, qc_and_assembly_data, mlst_data, acquired_amr_data and point_amr_data
make_microreact_metadata( epi_data, ast_data, qc_and_assembly_data, mlst_data, acquired_amr_data, point_amr_data, sample_ids = NULL, present_colour = "#ff6b6b", absent_colour = "#efefef", max_number_genes = 5, epi_data_columns = NULL, ast_data_columns = c("Sample id", "AST profile"), qc_and_assembly_data_columns = c("Sample id", "Bactinspector species", "Quast num contigs", "Quast N50", "Quast Total length"), mlst_data_columns = c("Sample id", "ST", "profile") )
| epi_data | A dataframe containing epidemiological data where 'Sample id' is the key |
|---|---|
| ast_data | A dataframe containing antimicrobial susceptibility data where 'Sample id' is the key |
| qc_and_assembly_data | A dataframe containing the outputs from the qc and assembly pipeline where 'Sample id' is the key |
| mlst_data | A dataframe containing the outputs from the MLST pipeline where 'Sample id' is the key |
| acquired_amr_data | A dataframe containing the acquired gene output from the AMR prediction pipeline where 'Sample id' is the key |
| point_amr_data | A dataframe containing the point gene output from the AMR prediction pipeline where 'Sample id' is the key |
| sample_ids | Default is NULL. If a last is given only those rows where 'Sample id' matches one of the ids specified in the list will be returned |
| 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 |
| epi_data_columns | The columns to be used in the output from the epidemiological data Defaults are 'Sample id', 'Alternative sample id', 'Year', 'Month', 'Day', 'Country', 'Location', 'Latitude', 'Longitude' |
| ast_data_columns | The columns to be used in the output from the antimicrobial susceptibility data Defaults are 'Sample id', 'AST profile' |
| qc_and_assembly_data_columns | The columns to be used in the output from the qc and assembly pipeline outputs Defaults are 'Sample id', 'Bactinspector species', 'Quast num contigs', 'Quast N50', 'Quast Total length' |
| mlst_data_columns | The columns to be used in the output from the MLST pipeline outpurs Defaults are 'Sample id', 'ST', 'profile' |
A dataframe combining all the data and where the 'Sample id' column is renamed to 'id' to make it compatible with microreact