mapping_dna_plot: Mapping the viral read hits to the reference
In jkruppa/virDisco: Modules for a viral detection pipeline

Description Usage Arguments Details Author(s)

A plotting function for the mapping results of the found viral strains

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mapping_dna_plot(genebank_id, consensus_df = NULL, dna_alignment_df,
  pep_alignment_df, aa_info_df, viral_info_df, sample_info = NULL,
  pdf_file = NULL, par_list)

`genebank_id`	Genebank IDs of the hits
`consensus_df`	Consensus data frame generated by `get_consensus_df`
`dna_alignment_df`	DNA alignment data frame generated by `map_dna_ref`
`pep_alignment_df`	AA alignment data frame generated by `map_pep_ref`
`aa_info_df`	SQLlite database from the `setup_aa_info_sample_sqlite`
`viral_info_df`	SQLlite database from the `setup_species_info_sqlite`
`sample_info`	Sample info data frame generated by `build_sample_info`
`pdf_file`	The output file, where the plot should be saved
`par_list`	Parameter given by the par_list(), see `set_par_list`

This is a realtivly complex function. First the genebank hit ids must be provided. All IDs, which are provided, must be found in the other options. Second a potential consensus data frame, where the consensus information of the reads to the viral reference is given, see get_consensus_df for more information. Then, the alignment of the DNA and AA mapping must be provided, see map_dna_ref and map_pep_ref for more information. Further, the SQLlite database for the viral info and the amino acid info must be given.

Jochen Kruppa

jkruppa/virDisco documentation built on May 3, 2019, 7:05 p.m.