Creates a pathway diagram for the kynurenine-tryptophan metabolic pathway with color-coded fold changes or correlations and significance indicators.
Usage
CreatePathwayPlot_KT(
results_table,
title = "",
value_type = "auto",
metabolite_mapping = NULL,
use_fdr = FALSE
)Arguments
- results_table
Data frame with columns: Metabolite, p_value, p_adj, and either "% Change" or "correlation"
- title
Character string for plot title
- value_type
Character string: "auto", "fold_change", or "correlation"
- metabolite_mapping
Named character vector mapping results table names to standard names. For example: c("N'-Formylkynurenine" = "N-Formylkynurenine", "Quinolinic Acid(log10)" = "Quinolinic Acid")
- use_fdr
Logical: if TRUE uses FDR-adjusted p-values (p_adj) for significance, if FALSE uses raw p-values. Default is FALSE.
Examples
if (FALSE) { # \dontrun{
# Basic usage with raw p-values
plot <- CreatePathwayPlot_KT(results, "My Pathway")
# Use FDR-adjusted p-values for significance
plot <- CreatePathwayPlot_KT(results, "My Pathway", use_fdr = TRUE)
# With custom metabolite name mapping
name_map <- c(
"N'-Formylkynurenine" = "N-Formylkynurenine",
"Quinolinic Acid(log10)" = "Quinolinic Acid",
"3-OH-kynurenine" = "3-Hydroxykynurenine"
)
plot <- CreatePathwayPlot_KT(results, "My Pathway", metabolite_mapping = name_map)
} # }