MAplotFromCts: Pairwise MA-plots using smoothScatter for QC purposes

In ATpoint/diffanalyseR: Wrapper functions for common tasks related to analysis of NGS counts data

Description

Given two vectors of normalized counts make an MA-plot to see how normalization performed and whether things look as expected.

Usage

MAplotFromCts(
  x,
  y,
  Plot.title = "",
  cts.arelog2 = FALSE,
  type = "base",
  abline0 = FALSE,
  abline2 = NULL,
  use.loess = FALSE,
  ...
)

Arguments

x	counts of sample1
y	counts of sample2
cts.arelog2	logical, whether counts are already on log2-scale
type	the type of the plot, currently only smoothScatter from base is available, later a ggplot version will come
abline0	logical, whether to add a horizontal ablone at y=0
abline2	numeric, add horizontal ablines at +/- abline2 value
use.loess	logical, whether to add a y ~ x loess fitted line
...	further arguments passed to smoothMAplot()

Details

the plot will be directly plotted to devise, so best would be to capture function directly to disk

Author(s)

Alexander Toenges

Examples

dds  <- estimateSizeFactors(makeExampleDESeqDataSet())
x <- counts(dds,normalized=TRUE)[,1]
y <- counts(dds,normalized=TRUE)[,2]
MAplotFromCts(x = x,y = y, use.loess=TRUE, Y.limits=c(-2,2))

ATpoint/diffanalyseR documentation built on Oct. 8, 2021, 10:11 p.m.