read_phy {ggmRSCU} | R Documentation |
Process PhyloSuite RSCU Data for Visualization
Description
Processes Relative Synonymous Codon Usage (RSCU) data from PhyloSuite CSV files, preparing it for visualization with the 'ggmRSCU' package.
Usage
read_phy(folder_path)
Arguments
folder_path |
Path to folder containing CSV files. Files must contain: - 'RSCU' column - Species-reflecting file names - Required columns: AA, Codon, Fill, RSCU |
Details
Performs:
File validation for required structure
Species name extraction
Data reshaping to long format
NA removal
Value
Visualization-ready data frame with:
- AA
Amino acid code
- Codon
RNA triplet
- Fill
Position index (1-6)
- Species
Organism identifier
- RSCU
Normalized usage values
Examples
# Using example data
example_dir <- system.file("extdata", "phy", package = "ggmRSCU")
result <- read_phy(example_dir)
head(result)
[Package ggmRSCU version 0.1.0 Index]