plot_pwy_ranef: Plot a pathway random effects result

In biobakery/anpan: Quantifying Microbial Strain-Host Associations

Plot a pathway random effects result

Description

Plot a pathway random effects result

Usage

plot_pwy_ranef(
  bug_pwy_dat,
  pwy_ranef_res,
  group_ind = "crc",
  group_labels = c("ctrl", "case"),
  bug_name = NULL,
  max_pwy = 20,
  post_draws = 30,
  verbose = TRUE
)

Arguments

bug_pwy_dat	a data frame with a row for each observation and columns "pwy", "log10_species_abd", "log10_pwy_abd", and a group indicator column named according to the group_ind argument
group_ind	a character giving the name of the column for the 0/1 group indicator variable in bug_pwy_dat
group_labels	labels for the 0/1 indicator to use on the plots
bug_name	name of the bug (if using a result from anpan_pwy_ranef())
max_pwy	the maximum number of bug:pwy facets to include
post_draws	number of post draws to draw in each facet
verbose	logical for verbosity

Details

This function plots bug:pwy data alongside posterior draws. If there's a strong group effect in a particular bug:pwy combination, you will see wide separation of the red and blue posterior lines.

If bug_name is specified, bug_pwy_dat is first filtered to just data from that bug.

If specified, bug_name must exactly match the corresponding entries in bug_pwy_dat.

biobakery/anpan documentation built on Aug. 14, 2024, 8:19 a.m.