explore: Explore MetAnnotate data

In MetAnnotate/metannoviz: Process and visualize output from the MetAnnotate pipeline

Description

high-level exploration function for examining MetAnnotate data

Usage

explore(
  metannotate_data,
  evalue = 1e-10,
  taxon = "Family",
  normalizing_HMM = "rpoB",
  top_x = 0.02,
  percent_mode = "within_sample",
  colouring_template_filename = NA,
  quietly = FALSE,
  ...
)

Arguments

metannotate_data	The mapped metannotate tibble output by map_naming_information
evalue	E-value cutoff for HMM hits
taxon	Character vector (length 1) giving the taxon name to collapse to Can be: domain, phylum, class, order, family, genus, species (case insensitive)
normalizing_HMM	Name of the normalizing HMM (e.g., 'rpoB')]; specify 'auto' to attempt auto-detection
top_x	Numeric vector (length 1) giving the subsetting amount you desire. If top_x >=1, the script will return the "top_x most abundant taxa" for each Dataset/HMM.Family If top_x <1, the script will return "all taxa of (top_x * 100%) abundance or greater for each Dataset/HMM.Family - but see below.
percent_mode	If top_x <1, there are two different methods for keeping the most abundant organisms: "within_sample" – the normalized % abundance relative to rpoB is used "within_HMM" – the percent abundance of that taxon within the specific HMM gene hits is used. You won't notice much of a different between these modes unless one of your HMMs has very few hits and you want to show some of the taxa that were hit. This would be a good time to use 'within_HMM'.
colouring_template_filename	Filename of the colouring template you want to load If the file does not exist, then this function will write a template to that file If 'NA' is entered, then the function will auto-generate colours and continue on
quietly	logical (TRUE/FALSE); if TRUE, only reports warnings and errors
...	Other fine-tuned plotting options controlled by visualize and the underlying generate_ggplot. Highlights include plot_type, which can be "bar" or "bubble"

Value

A ggplot of MetAnnotate data

MetAnnotate/metannoviz documentation built on Aug. 2, 2020, 3:12 p.m.