explore_mutations: MixviR Shiny Dashboard
In MixviR: Analysis and Exploration of Mixed Microbial Genomic Samples

View source: R/app.R

explore_mutations

R Documentation

MixviR Shiny Dashboard

Description

Open dashboard to explore mutation data generated with call_mutations().

Usage

explore_mutations(
  muts.df,
  dates = NULL,
  lineage.muts = NULL,
  read.muts.from = NULL,
  all.target.muts = FALSE
)

Arguments

`muts.df`	A data frame (produced by `call_mutations()`) storing mutation information for samples to analyze. Must contain columns SAMP_NAME, CHR, POS, GENE, ALT_ID, AF, & DP. Alternatively, the mutation data can be read in from a (tab-separated) file with the `read.muts.from()` argument. See also the write.mut.table argument in `call_mutations()`.
`dates`	Path to optional csv file with cols "SAMP_NAME", "LOCATION", and "DATE". Sample names need to match those in the muts.df data frame created by `call_mutations()`. Dates should be provided in the format mmddyyyy.
`lineage.muts`	Path to optional csv file with required cols "Gene", "Mutation", and "Lineage" defining mutations associated with lineages of interest. See example file at "https://github.com/mikesovic/MixviR/blob/main/mutation_files/outbreak_20211202.csv". Additional columns will be ignored.
`read.muts.from`	An alternative to muts.df for providing mutation input. If a data frame generated by `call_mutations()` was previously written to a (comma separated) file (see write.mut.table in `call_mutations()`), the mutation data can be read in from that file by providing its path. The fields "SAMP_NAME, CHR, POS, GENE, ALT_ID, AF, DP" must be present (additional fields will be ignored).
`all.target.muts`	Logical to indicate whether results for all target mutations were written to the output of the `call_mutations()` function. See write.all.targets option in `call_mutations()`. Default FALSE. If TRUE, more informative sequencing depth information can be provided in the dashboard.

Value

Shiny Dashboard to Explore Data

Examples

if (interactive()) {explore_mutations(read.muts.from = system.file("extdata", 
                                                                   "sample_mutations.csv", 
                                                                   package = "MixviR"),
                                      lineage.muts = system.file("extdata", 
                                                                 "example_lineage_muts.csv", 
                                                                 package = "MixviR"))}
if (interactive()) {explore_mutations(read.muts.from = system.file("extdata", 
                                                                   "sample_mutations.csv", 
                                                                   package = "MixviR"), 
                                      dates = system.file("extdata", 
                                                          "example_location_date.csv", 
                                                          package = "MixviR"), 
                                      lineage.muts = system.file("extdata", 
                                                                 "example_lineage_muts.csv", 
                                                                 package = "MixviR"))}

MixviR documentation built on Oct. 23, 2022, 1:09 a.m.