plotNorm: Function plotNorm

In jrthompson54/DGE.Tools2: A function library to facilitate Differential Gene Expression Analysis

Description

Takes a DGEobj (containing counts) or a counts matrix as input. Returns a ggplot object containing a faceted plot of log2CPM before/after normalization. Either a box plot or density plot type can be chosen.

Usage

plotNorm(dat, plotType = "box", normalize = "tmm", baseFont = 12)

Arguments

dat	A DGEobj or counts matrix
plotType	One of "box" or "density" (default="box")
normalize	Default = "TMM" and invokes TMM normalization. Other allowed values are: "RLE","upperquartile", "none". Invokes edgeR::calcNormFactors for normalization.
baseFontSize	Passed on as base font size in ggplot theme. (default=12)

Details

Normalization is performed by edgeR::calcNormFactors. Note TMM is specifically tailored to count-based data. Thus this function is only appropriate for count-based data.

Value

A facetted ggplot plot showing before/after normalization

Author(s)

John Thompson, [e-mail]

Examples

   MyggPlot <- plotNorm(MyDgeObj, plotType="box")
   MyggPlot <- plotNorm(counts, plotType="density")

jrthompson54/DGE.Tools2 documentation built on May 12, 2021, 8:47 p.m.