Swimmer Plot Scripts

Overview

The swimmer folder contains R scripts designed to create swimmer plots for visualizing treatment timelines and related data. These scripts process input data, calculate time differences, and generate swimmer plots for single and multiple treatments. The plots are saved as PDF or PNG files for further analysis and reporting.

Scripts

1. swimmer_single_treatment.R

Description

This script generates swimmer plots for single-treatment data. It processes input data, calculates time differences, and creates a swimmer plot with various visualizations, including treatment timelines and assay types.

Features

• Processes input data to calculate time differences.

• Generates swimmer plots for single-treatment data.

• Supports multiple time units (days, weeks, months, years).

• Saves the plot as a PDF file.

Arguments

Argument	Type	Description	Default Value
-i, --input	character	File path to the input data file.	None
-o, --output	character	File path for the output PDF file.	None
-t, --timeunit	character	Time unit for the x-axis (days, weeks, months, years).	days

Example Command

Rscript swimmer_single_treatment.R -i input_data.txt -o output_plot.pdf -t days

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2. swimmer_multi_treatment.R

Description

This script generates swimmer plots for multi-treatment data. It processes metadata, calculates time differences, and creates a swimmer plot with treatment timelines and ctDNA detection points.

Features

• Processes metadata to calculate time differences.

• Generates swimmer plots for multi-treatment data.

• Supports multiple time units (days, weeks, months, years).

• Allows customization of treatment colors.

• Saves the plot as a PNG file.

Arguments

Argument	Type	Description	Default Value
-m, --metadata	character	File path to the metadata file.	None
-o, --resultsdir	character	Output directory for the plot.	None
-c, --colors	character	Comma-separated colors for treatment types.	blue,red,green,yellow
-t, --timeunit	character	Time unit for the x-axis (days, weeks, months, years).	days

Example Command

Rscript swimmer_multi_treatment.R -m metadata.xlsx -o /path/to/output -c blue,red,green -t weeks

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3. dates2days.R

Description

This script converts date columns in the input data to numeric values representing time differences in specified units. The processed data is saved as a tab-delimited text file for use in swimmer plots.

Features

• Converts date columns to numeric time differences.

• Supports multiple time units (days, weeks, months, years).

• Saves the processed data as a tab-delimited text file.

Arguments

Argument	Type	Description	Default Value
-i, --input	character	File path to the input .txt file.	None
-o, --output	character	File path for the output .txt file.	None

Example Command

Rscript dates2days.R -i input_data.txt -o output_data.txt

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Requirements

R Packages

The scripts require the following R packages:

• dplyr

• ggplot2

• lubridate

• argparse

• readr

• readxl

• tidyr

• scales

• gridExtra

• cowplot

Install the required packages using the following command:

install.packages(c("dplyr", "ggplot2", "lubridate", "argparse", "readr", "readxl", "tidyr", "scales", "gridExtra", "cowplot"))

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Input File Requirements

Single Treatment Input File

The input file for swimmer_single_treatment.R must contain the following columns:

• collection_date

• start

• endtouse

• reason

• assay_type

• clinical_or_research

Multi-Treatment Metadata File

The metadata file for swimmer_multi_treatment.R must contain the following columns:

• start

• end

• collection_date

• treatment

• ctdna_detection

Dates to Days Input File

The input file for dates2days.R must contain date columns such as:

• pre_tx_date

• start

• end

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Outputs

Swimmer Plots

• Single Treatment: PDF file containing the swimmer plot.

• Multi-Treatment: PNG file containing the swimmer plot.

Processed Data

• Tab-delimited text file with numeric time differences for use in swimmer plots.

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Example Workflow

1. Convert Dates to Days:

   Rscript dates2days.R -i input_data.txt -o processed_data.txt

2. Generate Single Treatment Swimmer Plot:

   Rscript swimmer_single_treatment.R -i processed_data.txt -o single_treatment_plot.pdf -t days

3. Generate Multi-Treatment Swimmer Plot:

   Rscript swimmer_multi_treatment.R -m metadata.xlsx -o /path/to/output -c blue,red,green -t weeks

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Contact

For questions or issues, please contact:

• Author: Carmelina Charalambous, Alexander Ham

• Date: 11/30/2023