rottenice
Data processing python scripts used for the Rotten Ice project by Carie Frantz cariefrantz@weber.edu
List of scripts
| Script | Description | Data files used |
|---|---|---|
| AlphaDiversityPlots.py | Used to generate alpha diversity metric boxplots from rarefied sequencing sample metrics | alpha_diversity_metrics_16S.csv, alpha_diversity_metrics_18S.csv |
| BetaClustermaps.py | Used to generate sample clustermaps from sample distance matrices | 16S_dist_matrix.csv, 18S_dist_matrix.csv |
| ChemDataPCA.py | Used to generate PCA plots of physical and chemical habitat parameters | metadata.csv |
| ChemHeatmaps.py | Used to generate heatmaps of sample metadata (physical, chemical, and biological measurements) | metadata.csv |
| SpearmanGrid.py | Used to generate a heatmap grid of Spearman correlation coefficients for metadata vs. taxonomic group abundance | metadata.csv, 16S_cDNA_ASV-table.csv, 18S_cDNA_ASV-table.csv |
| WebTaxBarplotsSimple.py | Used to generate interactive side-by-side bokeh taxonomic bar plots (web-based) from algae taxonomy data. Results at different taxonomic levels are built in as tabs. | AlgaeIDs.csv |
| WebTaxBarplotsStacked.py | Used to generate interactive stacked bokeh taxonomic bar plots (web-based) from Illumina sequencing data. Plots for absolute and relative abundance for both DNA and cDNA are stacked for ease of comparison. | 16S_DNA_ASV-table.csv, 16S_cDNA_ASV-table.csv, 18S_DNA_ASV-table.csv, 18S_cDNA_ASV-table.csv |
Shared scripts
The following scripts are called by several (most) of the main scripts listed above. Download these to the same directory as the scripts above.
| Script | Description |
|---|---|
| RottenIceModules.py | Collection of scripts shared by multiple other scripts in this project |
| RottenIceVars.py | Collection of variables shared by multiple other scripts in this project |
Setting up
The code for this project requires the following list of packages in order to run.
- tkinter
- progress
- numpy
- pandas
- math
- scipy
- sklearn
- seaborn
- matplotlib
- bokeh
To install using conda, execute the command:
conda install tkinter
conda install progress
...and so on
To install using pip, execute the command:
pip install tkinter
pip install progress
...and so on
Running
Once python and the packages listed above are installed, to run a script from command line execute the command:
python ChemDataPCA.py
python WebTaxBarplotsSimple.py
...and so on