multi_hit_calling_plot: Show hit-calling metrics for multiple interactions
In andrewGhazi/basehitmodel: Runs the basehit ZINB model

multi_hit_calling_plot

R Documentation

Show hit-calling metrics for multiple interactions

Description

Plot both the posterior intervals of interaction score and position in the concordance distribution

Usage

multi_hit_calling_plot(
  ixns = c("CD55:AIEC", "CEACAM1:AIEC", "CD7:AIEC", "CEACAM1:NWP04"),
  bead_binding,
  concordances,
  fit_summary,
  name_df = NULL,
  weak_score_threshold = 0.5,
  strong_score_threshold = 1,
  weak_concordance = 0.75,
  strong_concordance = 0.95,
  global_entropy = FALSE,
  tags = TRUE,
  intervals = c(0.95, 0.99)
)

Arguments

`ixns`	a character string giving multiple interactions as protein:strain
`bead_binding`	bead-binding enrichment dataframe (saved as part of all_outputs.RData)
`concordances`	concordance dataframe (saved as part of all_outputs.RData)
`fit_summary`	the interaction score summary dataframe (result from basehitmodel::model_proteins_separately())
`name_df`	a dataframe giving the strain identifiers and taxonomic names in two columns: "strain" and "strain_name"
`weak_score_threshold`	score threshold for calling weak hits
`strong_score_threshold`	score threshold for calling strong hits
`weak_concordance`	concordance threshold for weak hits
`strong_concordance`	concordance threshold for calling strong hits
`global_entropy`	logical indicating whether to show the global entropy histogram of all profiled interactions (TRUE) or only interactions with scores that exclude 0 by the narrower interval (default FALSE)
`tags`	logical: show A & B on the two panels?
`intervals`	amount of probability mass to include in the two intervals