Dot plots based on edgeR results for microbiome data — plot

Plots results of get_edgeR_results_all_levels() using the ggplot2 engine.

Usage

plot_edgeR(
  formla,
  ttle = NULL,
  varname = NULL,
  pseq = NYC_HANES,
  coef = 2,
  printIfEmpty = FALSE,
  invisbl = FALSE,
  color = "FDR",
  sortby = NULL,
  ...
)

Arguments

formla: formula. specifies the design matrix used by edgeR::glmFit.
ttle: character. Title of plot.
varname: character. Label for independent variable, for plotting.
pseq: object of class phyloseq
coef: integer. Specifies which linear model coefficient to test (default 2).
printIfEmpty: logical. If no results pass alpha, whether or not to plot an empty plot.
invisbl: logical. Whether or not to forgoe plotting. Either way, invisibly returns the topTags object returned by get_edgeR_results.
color: character. Variable to color by, from either the tax_table or the topTags$table.
sortby: character. Variable to sort the plot by, from either the tax_table or the topTags$table.
...: further arguments passed to get_edgeR_results.