make_MA: Create MA plot

In anilchalisey/rseqR: RNA-seq data processing pipeline

Description

Create a scatter plot of log2 fold changes vs the mean expression signal.

Usage

make_MA(data, fdr = 0.05, label.rectangle = FALSE,
  proc = c("Limma-voom", "edgeR", "DESeq2"), top = 0,
  select.method = c("padj", "logfc"), main = NULL)

Arguments

data	matrix or data.frame with the columns for average gene expression, adjusted P-value, and log fold change; created as part of edger_analysis, limma_voom_analysis, or deseq2_analysis.
fdr	numerical value between 0 and 1 indicating the threshold false discovery rate for discovering differentially expressed genes. [DEFAULT = 0.05]
label.rectangle	logical indicating whether to add rectangles underneath gene names [DEFAULT = FALSE]
proc	character string indicating analysis procedure used. One of "Limma-voom", "edgeR", "DESeq2". [DEFAULT = "Limma-voom].
top	integer indicating the number of genes to label
select.method	Character string identifying the method of selecting the top genes. One of padj or logfc
main	character string giving the plot main title

Value

A ggplot2 object

anilchalisey/rseqR documentation built on May 25, 2019, 2:25 p.m.