Become Competent in Generating RNA-Seq Heat Maps in One Day for Novices Without Prior R Experience

Academic Article

Abstract

  • Heat map visualization of RNA-seq data is a commonplace task. However, most laboratories rely on bioinformaticians who are not always available. Biological scientists are afraid to prepare heat maps independently because R is a programming platform. Here, using RNA-seq data for 16 differentially expressed genes in WNT pathway between embryonic stem cells and fibroblasts, I share a tutorial for novices without any prior R experience to master the skills, in one day, required for preparation of heat maps using the pheatmap package. Procedures described include installation of R, RStudio, and the pheatmap package, as well as hands-on practices for some basic R commands, conversion of RNA-seq data frame to a numeric matrix suitable for generation of heat maps, and defining arguments for the pheatmap function to make a desired heat map. More than 20 template scripts are provided to generate heat maps and to control the dimensions and appearances of the heat maps.
  • Authors

    Published In

    Digital Object Identifier (doi)

    Author List

  • Hu K
  • Start Page

  • 269
  • End Page

  • 303
  • Volume

  • 2239