plotDE: Plots the differntially expressed genes on an MA plot, ggplot...

In hbc/CHBUtils: "Useful utility functions used at the core"

Description

Plots the differntially expressed genes on an MA plot, ggplot style If adjusted pvalues are present, colors those that pass cutoff red

Usage

plotDE(pvaldf, basemean_colid = NULL, log2foldchange_colid = NULL,
  adj_pval_colid = NULL, adj_pval_cutoff = 0.05, plottitle = "MA plot")

Arguments

pvaldf	dataframe, required
basemean_colid	character string, column header of column containing baseMean values, required
log2foldchange_colid	character string, column header of column containing log2 transformed fold change values, required
adj_pval_colid	character string,column header of column containing adjusted pvalues, required
adj_pval_cutoff,	optional, defaults to 0.05
plottitle	character string, title for the plot, optional, defaults to "MA plot"

Examples

plotDE(df, basemean_colid="baseMean",log2foldchange_colid=log2FoldChange, adj_pval_colid="padj", adj_pval_cutoff=0.05, plottitle="My MA plot")

hbc/CHBUtils documentation built on May 17, 2019, 3:07 p.m.