DEcompare: DEcompare
In amitjavilaventura/seqViewR: Visualization of Omics And Sequencing Data In R

DEcompare

R Documentation

DEcompare

Description

Function that takes a list of 2 dataframes with expression data and compares the log2FoldChange values of the two data sets.

Usage

DEcompare(
  deg_list,
  threshold = 1.5,
  genes = NULL,
  xlim = c(-10, 10),
  ylim = c(-10, 10),
  xlab = "Contrast1",
  ylab = "Contrast2",
  main = "Comparison of Log2FC",
  subtitle = paste(xlab, "vs", ylab),
  color_corners = c("pink", "lightgreen", "cornflowerblue", "yellow"),
  alpha_corners = c(0.7)
)

Arguments

`deg_list`	List of lenght 2. Must contain data frames with the columns Geneid, log2FoldChange, padj and DEG. Values in 'Geneid' must be the same in both data frames.+
`threshold`	Numeric of lenght 1. Threshold for the log2FoldChange. It is used to draw horizontal and vertical lines. Default: 1.5.
`genes`	Charachter of indefined lenght or NULL. Genes to be written in the plot. Default: NULL.
`xlim`	Numeric of length 2. The limits of the Y axis. Default: c(-10, 10)
`xlab`	Character of lenght 1. Name of the X axis. Default: "Contrast1"
`ylab`	Character of lenght 1. Name of the Y axis. Default: "Contrast2"
`subtitle`	Character of lenght 1. Subtitle of the plot. Default: paste(xlab, "vs", ylab)
`alpha_corners`	Numeric of length 1 to 4. If too short, it will be recycled. Alpha (transparency) value for the vars. Default: 0.7
`title`	Character of lenght 1. Title of the plot. Default: "Comparison of Log2FC"
`colors`	Character of length 1 to 4. If too short, it will be recycled. Colors for each of the corners: top-left, bottom-left, top-right, bottom-right. Default: c("pink", "lightgreen", "cornflowerblue", "yellow")