plot_lines: Make a filter-labelled line plot

In biobakery/anpan: Quantifying Microbial Strain-Host Associations

Make a filter-labelled line plot

Description

Make a filter-labelled line plot

Usage

plot_lines(
  bug_file = NULL,
  meta_file = NULL,
  covariates,
  outcome,
  genomes_stats,
  omit_na = FALSE,
  fgf = NULL,
  bug_name = NULL,
  plot_ext = "pdf",
  plot_dir = NULL,
  subset_line = 200
)

Arguments

bug_file	a path to a gene family file
meta_file	a path to the corresponding metadata file
covariates	covariates to account for (as a vector of strings)
outcome	the name of the outcome variable
omit_na	logical indicating whether to omit incomplete cases of the metadata
fgf	a filtered gene family data frame
bug_name	name of the bug
plot_ext	extension to use for plots
subset_line	integer gives the number of points to take along the lines

Details

The required input is either

• the gene family file and the metadata file

• OR a pre-filtered gene family file

subset_line is used to make saving plots faster. Plotting thousands of lines each with tens of thousands of points along them is too much visual detail and makes saving the plot very slow. Set subset_line to 0 to turn off subsetting.

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