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Create Project Folder Structure

Source: R/create_folders.R
create_folders.Rd

This function creates a folder structure for projects, ensuring that all necessary directories exist and that specific files required for downstream analyses are present.

Usage

create_folders(projects)

Arguments

projects

A character vector containing the names of the project (folders).

base_path

A character string indicating the base directory where the project folders are located. This path is used to locate the project folder and create the required subfolders.

log_file

A character string specifying the path to the log file where warnings and errors will be recorded.

Value

None. This function is called for its side effects.

Details

This function facilitates the setup of downstream analyses by:

  • Creating a consistent directory structure for each project, including subfolders such as input_data, output_data, figures, and messages.

  • Copying essential files from the qiime2_output folder into the input_data folder. These essential files include:

    • table.qza: The feature table from QIIME2.

    • rooted-tree.qza: The phylogenetic tree used for diversity analysis.

    • classifier.qza: The classifier used for taxonomy assignment.

    • metadata.tsv: The QIIME2 sample metadata file required for analyses.

    • metadata_extra.tsv: Any additional metadata provided for the samples.

    • pantaxa_stats_NCBI.tsv: The reference database for copy number correction from rrndb.

    • prediction.RDS: The predicted 16S copy numbers for each feature.

  • Checking for optional files that enhance analyses, such as:

    • qPCR.csv: Contains quantitative PCR data.

    • fcm.csv: Contains flow cytometry data.

  • Logging warnings for missing optional files and errors for missing required files.

The function ensures that downstream analyses—which rely on specific input files (e.g., table.qza, rooted-tree.qza, etc.) have access to these files in the correct directory structure. If any required files are missing from the qiime2_output folder, the function stops execution and logs an error message.

Note

Each project folder must already exist within the base_path directory and must contain a subfolder named qiime2_output, which holds the outputs of QIIME2 analysis and other necessary files. The function sets up the folder structure for downstream analysis within this project folder.

Examples

if (FALSE) { # \dontrun{
# Define the base path and log file location
projects <- "project_name"
base_path <- "path/to/projects"
log_file <- "path/to/log_file.log"

# Create folder structures for projects
create_folders(projects)
} # }