A series of two scripts (python and R) along with instructions and sample data from Jahnke et al., (2015), that will enable you to create colour gradient maps of genetic diversity of the seagrass Posidonia Oceanica in the Meditteranean Sea. In addition, there is sample data of a scale of cumulative human impacts from Micheli et al.,(2013). Combining both data sets, interesting and informative maps can be achieved.
First download data and reformat in gedit. The python script calls upon the desired genetic/human impact variable to run. The output of the python script is saved in the current working directory. The R script is created with the relevant functions and packages installed to create the maps and then saved. From the shell the relevant modules are loaded and the python and R scripts are executed. A map is created as a result each time.
- Genetic diversity map: This displays 56 populations of Posidonia. Each of population data points is given a colour based on level of genetic diversity- the darker the colour, the higher the diversity. This is displayed on a colour gradient legend.
- Human impact map: Twelve various human impacts are chosen from (Micheli et al., 2013) all from the Meditteranean Sea. The colour gradient dipicts areas of high human impact to areas of low human impact. The colours can be contrasted against the size of the genetic diversity data point (which each represent a population of posidonia, the larger the circle- the higher genetic diversity) and you can see if there is any correlations between different human impacts and degree of genetic diversity.
If you wish, you may clone this repository and try it for yourself! https://github.com/Aoife10/PCfB-Project.git