README

BRICKPLOTS USER GUIDE

Preliminary setup

The following packages are required to run brickplots:

"scales"
"spatial"
"RColorBrewer"
"viridis"
"plotrix"
"factoextra

These can all be install from the cran repository using the install.packages("package_name") command. 
If prompted, select "yes"/"y" to installing any dependencies or compiling any packages. 
If on a Mac, you will also need to download and install Xcode prior to installing these packages.
Follow this link to download Xcode - https://apps.apple.com/us/app/xcode/id497799835?mt=12


1. Download the script in this GitHub repository named brick_plots.R
2. Open the script in R/Rstudio or equivalent
3. Navigate to your working directory (and set it as such) containing you dataset which should be in the following format, as a .csv file.

Cluster ID   Marker 1  Marker n
#0001         4.903     3.289
#0002	        1.876     2.783
#...n         2.346     0.896


4. Select the entire script and run it
5. The script will prompt you to select your data file, select it and click okay.
6. The plots will generate automatically from this point and save to a new images folder

###########NOTES############

Line 54 of the code grants the option to change how many clusters are formed for colouring the included markers. 
This can be set manually based on the elbow point plot included as the first generated figure.

Line 234 of the code grants the option to change the minimum value for a brick to be created, this is essentially
setting the background threshold and may need to be altered to suit your dataset.