RNAseqQC (version 0.2.1)

plot_ma: MA-plot of a differential testing result

Description

MA-plot of a differential testing result

Usage

plot_ma(de_res, dds, annotate_top_n = 5, highlight_genes = NULL)

Value

A ggplot object of the ggplot2 package that contains the MA-plot. The plot shows three classes of points: Light gray points are genes with low counts that are removed from the analysis by independent filtering. Darker gray points are not significant genes that show a density map to visualize where the majority of non-significant points are located. Finally, red point show significant genes.

Arguments

de_res

An object returned by DESeq2::results() or DESeq2::lfcShrink()

dds

The DESeqDataSet that was used to build the ´de_res´ object. This is needed for gene name annotation.

annotate_top_n

Annotate the top n significant genes by fold change (up- and down-regulated)

highlight_genes

Vector of gene names or gene IDs to highlight on the plot (overwrites top_n annotation)

Examples

library("DESeq2")
set.seed(1)
dds <- makeExampleDESeqDataSet(n=1500, m=6, betaSD=.3, interceptMean=6)
rowData(dds)$gene_name <- rownames(dds)
dds <- DESeq(dds)
de_res <- results(dds)
plot_ma(de_res, dds)