Description Usage Arguments Details Author(s)
A plotting function for the mapping results of the found viral strains
1 2 3 | 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
|
dna_alignment_df |
DNA alignment data frame generated by
|
pep_alignment_df |
AA alignment data frame generated by
|
aa_info_df |
SQLlite database from the
|
viral_info_df |
SQLlite database from the
|
sample_info |
Sample info data frame generated by
|
pdf_file |
The output file, where the plot should be saved |
par_list |
Parameter given by the par_list(), see
|
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
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