Generating Heatmaps in R - Workshop

This is the Github repository for the event - minisciencegirl/studyGroup#47. The official event details are as follows:

• Date: September 8, 2015
• Time: 5:30pm
• Room: BCCA (Dorothy Lam Room)

Preparation for the Workshop

The workshop will contain coding exercises where you can run R code to generate some heatmaps. If you are interested in doing this, please bring your laptop to the workshop and do the following preparation steps.

1. git clone this repository:

   git clone git@github.com:tinyheero/R-Heatmaps.git
   

   The repository comes with the following files/folders:

   • Generating-Heatmaps-in-R.pdf: This is the slidedeck for the workshop.
   • heatmap-cluster.Rmd: This is an Rmarkdown file that contains a tutorial and code on how to generate the images shown in the slide deck.
   • heatmap-cluster.html: The final output of heatmap-cluster.Rmd.
   • data: Folder containing the data files required for the heatmap-cluster.Rmd file.

   If you are unable to git clone this repository, you can also download a packaged version of this repository through the releases link (at the top). Please contact me if you are having trouble with either step.

2. Install Rstudio (if you haven't already). The code was tested to work with RStudio 0.99.484.

3. Inside of Rstudio, make sure you install the following R packages (the version numbers of each package have been provided to indicate what they were tested on to work with)

   • dplyr (v0.4.3)
   • knitr (v1.11)
   • d3heatmap (v0.6.1)
   • RColorBrewer (v1.1-2)
   • reshape2 (v1.4.1)
   • ggplot2 (v1.0.1)

   Packages can be installed using the install.packages function. For example:

   install.packages("dplyr")
   

4. Make sure you can render the heatmap-cluster.Rmd file by opening the heatmap-cluster.Rmd file in RStudio and then pressing the "Knit HTML" button. If it works, then you should see a separate window open with a document titled "Generating Heatmaps in R".

FAQ

1. Why can't I load the mat.lim variable?

   This is likely occurring because the data/mirna-normalized-expression-subset-lim-2015.txt file is missing or R can't find the file. If you are using the RStudio to open the heatmap-cluster.Rmd, you need to make sure that the working directory of your R contains both the heatmap-cluster.Rmd and data/mirna-normalized-expression-subset-lim-2015.txt. Specifically, the text file needs to be in a data folder.

   The best procedure is git clone the repository or download the release package, open heatmap-cluster.Rmd in RStudio, then at the top go Session -> Set Working Directory -> To Source File Location.

Contact

Feel free to contact me for help regarding the content in this workshop:

• email: fongchunchan@gmail.com
• twitter: https://twitter.com/fongchunchan
• blog: http://tinyheero.github.io/