shinyDECorr: Create an interactive Shiny app for correlation of...

In j-andrews7/iBET: Interactive Bioinformatics Exploratory Tools

Create an interactive Shiny app for correlation of differential expression results

Description

This shiny app generates scatter plots for every combination of DE results fed to it. It is useful for comparing relative differences in differential expression for common conditions between different backgrounds, groups, or settings.

Usage

shinyDECorr(
  res,
  sig.col = NULL,
  sig.thresh = 0.05,
  lfc.col = NULL,
  gene.col = NULL,
  expr.col = NULL,
  genesets = NULL,
  height = 800
)

Arguments

res	Either a named list of data.frames containing differential expression analysis results or a named list of such lists. The list of lists approach allows the user to choose between different comparison sets.
sig.col	String for the column name of the significance value, e.g. "padj". If not provided, the function will search for commonly used values ("padj", "FDR", "svalue", "adj.P.Val") in the column names.
sig.thresh	Number to be used as the significance threshold. Adjustable within the app.
lfc.col	String for the column name of the log2 fold change column, e.g. "log2FC". If not provided, the function will search for commonly used values ("log2FoldChange", "logFC", "LFC") in the column names.
gene.col	String for the column name containing the gene identifier. If not provided, rownames will be used.
expr.col	Optional string for the column name containing average expression. If not provided, the function will search for commonly used values ("baseMean", "logCPM", "AveExpr") in the column names.
genesets	Optional named list containing genesets that can be interactively highlighted on the plots. The elements of the list should each be a geneset with gene identifiers matching those used in the results.
height	Number indicating height of app in pixels.

Details

Gene labels can be added to the plots by clicking a point. The labels can also be dragged around, though adding labels to a plot will reset the positions, so it's recommended to add all labels prior to re-positioning them.

Comparisons will be limited to shared genes.

Value

A Shiny app containing scatter plots comparing all combinations of the DE results to each other, along with a line of best fit, correlation testing, gene and geneset highlighting, and movable annotations.

Author(s)

Jared Andrews

j-andrews7/iBET documentation built on April 17, 2025, 2:55 p.m.