scanner_output: Output a markdown for scanner results, including full written...

In emvolz-phylodynamics/variantAnalysis: sarscov2 variant analysis

Usage

scanner_output(
  lineages = "B.1.525",
  mutations = NULL,
  cut_off = NULL,
  path_to_scanner = "../min_25/3_month/",
  scanner_run_date = "2021-03-19",
  path_to_data = "../",
  path_to_metadata = NULL,
  log_growth_rate_cut_off = 0,
  defining_mutations_cut_off = 90,
  prop_mutation = 25,
  path_to_save = NULL,
  min_size = 25,
  max_size = 20000,
  max_date = "2021-03-04",
  min_date = "2020-11-01",
  include_pillar1 = FALSE,
  generation_time = 6.5,
  prop_cluster = 10
)

Arguments

lineages	Lineage of interest, if NULL not used for inclusion criteria
mutations	Mutations of interest, if NULL not used for inclusion criteria
cut_off	Statistical cut off of interest, if NULL not used for inclusion criteria. If growth rate below 5 selected, will use this as a Growth rates > x cut off. If cut_off >= 5 selected, will return the clusters with top x growth rates.
path_to_scanner	Path to scanner run outputs and scanner metadata (scanner.rds, scanner.csv & scanner_env)
path_to_data	Path to COG tree and COG tree metadata (sample_date, )
path_to_metadata	Path to sequence metadata (age, gender) e.g. PHE data, if NULL no age plots included
log_growth_rate_cut_off	Logistic growth rate cut-off we use as exclusion criteria
defining_mutations_cut_off	Minimm proportion ( of sequences in comparison general population cluster that must have a specific mutation for it to be considered a defining mutation of a cluster of interest
prop_mutation	Proportion of sequences ( \item path_to_savePath to directory to save markdown in, if NULL will save in current working directory \item max_dateMost recent tip sample date from scanner run \item min_dateLeast recent tip sample date from scanner run \item prop_clusterProportion of cluster ( Currently includes cumulative sum of sampled sequences, logistic growth rate and frequency in log odds over time, coordinates of logistic growth rates, lineages/clusters of interest, samples dates, growth rates over time for lineages of interest, proportion of sequences with mutations of interest. Age proportions in cluster can be added (if scanner outputs stored locally and linked with PHE, to be added in...) TO ADD: treestructure figure linking growth rates to node number and p-value on tree for each cluster of interest Keep random sample of size N from tree with sequences from clusters of interest, node values on tree Clusters coloured using Dark2

emvolz-phylodynamics/variantAnalysis documentation built on Nov. 13, 2021, 7:16 p.m.