interMA: Interactive MA Plot

In kevincjnixon/BinfTools: Useful functions for standard analyses

Interactive MA Plot

Description

This function creates an interactive MA plot from a DESeq2 results object. It is like 'plotMA()' from DESeq2, but more customizable and interactive.

Usage

interMA(res, title = "MA Plot", p = NULL, pval = NULL, FC = 1)

Arguments

res	A DESeq2 results object obtained from 'results(dds)' or a data.frame with the same column name values as a DESeq2 results object and rownames as genes
title	A character vector indicating the title of the plot
p	A number indicating the threshold for 'padj' where padj<p are significant genes. Should not be used if using 'pval'
pval	A number indicating the threshold for 'pvalue' where pvalue<pval are significant genes. Should not be used if using 'p'
FC	A number indicating the log2FoldChange threshold where abs(log2FC)>FC are significant genes. Default is 1 - can be 0 if not using fold-change threshold.

Value

An interactive MA plot with x-axis indicating gene expression 'baseMean' and y-axis indicating log2FoldChange. Blue dots are downregulated genes, red dots are upregulated genes.

kevincjnixon/BinfTools documentation built on July 10, 2024, 11:46 a.m.