fold_enhancer_plot: Plot histogram for significant allele with all alleles as...

In WeirauchLab/mpraprofiler: Statistical Analysis and Visualization for MPRA Data

Plot histogram for significant allele with all alleles as background

Description

A quick plot to visualize the distribution of the significant alleles with all alleles as background. Yellow lines are added to indicate the fold change cut off.

Usage

fold_enhancer_plot(object, ...)

## S4 method for signature 'DESeqResults'
fold_enhancer_plot(
  object,
  alpha = 0.05,
  bw = 0.01,
  breaks = waiver(),
  foldchange = 0.5,
  yadjust = 100,
  ladjust = 0.25,
  radjust = 0.25,
  xmin,
  xmax,
  ymax,
  main = NULL
)

Arguments

object	a DESeqResults object produced by results
...	additional arguments
alpha	the significance level for thresholding adjusted p-values
bw	bandwidth
breaks	One of: - 'NULL' for no breaks - 'waiver()' for the default breaks computed by the transformation object - A numeric vector of positions - A function that takes the limits as input and returns breaks as output
foldchange	the fold change of the yellow line
yadjust	the y location of fold change text
ladjust	the adjustment for the left yellow line
radjust	the adjustment for the right yellow line
xmin	the minimum value for the x-axis
xmax	the maximum value for the x-axis
ymax	the maximum value for the y-axis
main	the title of the figure.

Examples

dds <- DESeqDataSetFromMatrix()
dds <- DESeq(dds)
res <- results(dds, contrast=c("condition","exp","ctrl"))
fold_enhancer_plot(res)

WeirauchLab/mpraprofiler documentation built on June 29, 2023, 11:56 p.m.