Deseq.quickplot: Quickly plot Deseq2 results

In Jtrachsel/funfuns: Functions I Use (Title Case)

Description

Should really split this into 2 functions, one that returns the results df with lfc shrinkage etc and another that plots...

Usage

Deseq.quickplot(
  DeSeq.object,
  phyloseq.object,
  pvalue = 0.05,
  name,
  taxlabel = "Genus",
  shrink_type = "normal",
  colors = NULL,
  scientific = FALSE,
  cookscut = FALSE,
  alpha = 0.05,
  LFC_cut = 0
)

Arguments

DeSeq.object	Deseq object that the desired pairwise contrast exists in
phyloseq.object	phyloseq object containing the taxonomy table associated with the OTUs in the Deseq object
pvalue	pvalue to filter results table with
name	the name of the results contrast you want to display
taxlabel	the taxonomy label to use for the plot labels (needs to be present in the tax table from the phyloseq object)
shrink_type	one of the methods used by the DEseq function lfcshrink
colors	optional. A vector of length 2, first value will be the color associated with the 2nd value from the contrast vector, 2nd value will be the color associated with the 3rd value from the contrast vector
scientific	do you want pvalues in scientific format?
cookscut	should we apply the cookscutoff parameter in DEseq2?
alpha	passed to DEseq2 results function
LFC_cut	filter results based on absolute value lfc? default=0

Value

returns a list containing: [[1]] a ggplot object, [[2]] a dataframe containing the significantly differentially abundant features

Examples

#soon

Jtrachsel/funfuns documentation built on Aug. 8, 2021, 7:31 p.m.