significant_barplots: Given the set of significant genes from combine_de_tables(),...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Given the set of significant genes from combine_de_tables(), provide a view of how many are significant up/down.

Description

These plots are pretty annoying, and I am certain that this function is not well written, but it provides a series of bar plots which show the number of genes/contrast which are up and down given a set of fold changes and p-value.

Usage

significant_barplots(
  combined,
  lfc_cutoffs = c(0, 1, 2),
  invert = FALSE,
  p = 0.05,
  z = NULL,
  p_type = "adj",
  according_to = "all",
  order = NULL,
  maximum = NULL,
  ...
)

Arguments

combined	Result from combine_de_tables and/or extract_significant_genes().
lfc_cutoffs	Choose 3 fold changes to define the queries. 0, 1, 2 mean greater/less than 0 followed by 2 fold and 4 fold cutoffs.
invert	Reverse the order of contrasts for readability?
p	Chosen p-value cutoff.
z	Choose instead a z-score cutoff.
p_type	Adjusted or not?
according_to	limma, deseq, edger, basic, or all of the above.
order	Choose a specific order for the plots.
maximum	Set a specific limit on the number of genes on the x-axis.
...	More arguments are passed to arglist.

Value

list containing the significance bar plots and some information to hopefully help interpret them.

Examples

## Not run: 
 expt <- create_expt(metadata = "some_metadata.xlsx", gene_info = annotations)
 pairwise_result <- all_pairwise(expt)
 combined_result <- combine_de_tables(pairwise_result)
 ## Damn I wish I were smrt enough to make this elegant, but I cannot.
 barplots <- significant_barplots(combined_result)

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.