DOC and Biomass Data Processing and Visualization

Overview

This repository contains the R code and data used to calculate Dissolved Organic Carbon (DOC) consumption (inlet - outlet) and visualize biomass cell counts for our paper. The workflow includes data cleaning, consumption calculations, and plot generation.

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Project Structure

├── data/ │ ├── DOC_consumption.csv # Calculated DOC consumption (inlet - outlet) │ └── DOC_per_column.csv # Raw DOC measurements (inlet/outlet) ├── output/ # Generated plots and processed data ├── R/ # R scripts for processing and plotting ├── LICENSE └── README.md

Data

Inputs

• data/DOC_final_pretreated_all.csv: Pretreated raw DOC measurements (µg C/L) for inlet/outlet samples across columns and time points.
• data/Cell_Counts_standardized.csv: Standardized biomass cell counts (10⁶ cells/L) for each column and time point.

Outputs

• Processed data and plots are saved in the output/ directory.

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Workflow

1. Data Processing and DOC Consumption Calculation

Script: R/Column_DOC_Calculations.R

• Loads data/DOC_final_pretreated_all.csv and data/Cell_Counts_standardized.csv.
• Calculates DOC consumption: consumption = inlet - outlet.
• Merges DOC consumption with biomass data.
• Saves processed data to output/.
• Generates faceted boxplots for:
  • DOC consumption vs. time.
  • Biomass vs. time.
• Adds annotations (a–j) to each facet for reference in the paper.
• Saves plots to output/.

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2. Plotting

Script: R/plotting_functions.R

• Holds the necessary functions to convert the labels and apply the global coloring scheme

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