plotDifferentialAbundanceOverview: plotDifferentialAbundanceOverview

In heuselm/igseqr: Integrate MiXCR BCR/IG-Seq and DIA-MS data to profile immune repertoire evolution

plotDifferentialAbundanceOverview

Description

Produce overview plots of multiple differential test results

Usage

plotDifferentialAbundanceOverview(
  diffExpr_result_dt,
  significance_threshold_p = 0.05,
  significance_threshold_fc = 2,
  label_prefix = NULL,
  remove_from_protein_names = "\\(Bos;|_MOUSE|_HUMAN",
  browsable_html = TRUE,
  protein_highlight_tag = "IGSeq",
  heatmap = TRUE
)

Arguments

diffExpr_result_dt	Input data table, typically appended result tables with differential expression testing results as produced by testDifferentialAbundance
significance_threshold_p	Significance threshold on p-value to be indicated in plots (p_value_BHadj_protein <= x)
significance_threshold_fc	Significance threshold on fold-change to be indicated in plots (|log2FC| >= log2(x)). A two-fold change is 2. The log2FC cutoff is then 1.
label_prefix	Prefix label for the output plots. Defaults to "(input R object name)_".
remove_from_protein_names	Regular expression of string components to remove from Protein.Names.
browsable_html	Whether brosable volcanoe plot .htmls are to be generated. Default: TRUE.
protein_highlight_tag	Substring of Protein names that get highlighted (color) in plots.
heatmap	Whether an overview heatmap of FCs is to be drawn for the proteins passing the p-value cutoff at least once.

Value

A (list) containing (access by x$ or by "x[[name]]")

• diffExpr_result_dt: Reduced diffExpr_result_dt processed for plots

• volcanos: Volcano plots as ggplot object

• heatmap: heatmap obj

• FC_matrix: matrix of Log2FCs of proteins passing the p-value significance threshold in any one of the comparisons

Author(s)

Moritz Heusel

heuselm/igseqr documentation built on March 19, 2022, 7:28 p.m.