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Add gprofiler2 intereactive plot to the Rmarkdown report #524

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Add gprofiler2 intereactive plot to the Rmarkdown report #524

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22 changes: 22 additions & 0 deletions assets/differentialabundance_report.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -1029,8 +1029,30 @@ if (!is.null(params$functional_method)){
name <- differential_names[i]
cat(paste0("\n##### ", name, "\n"))

plot_html <- paste0(contrasts$id[i], ".gprofiler2.gostplot.html")
plot_path <- file.path(params$input_dir, plot_html)

table <- paste0(contrasts$id[i], ".gprofiler2.all_enriched_pathways.tsv")
table_path <- file.path(params$input_dir, table)

# Check and include interactive plot
if (file.exists(plot_path) && file.size(plot_path) > 0) {
cat("\n**Interactive Pathway Enrichment Plot:**\n")
cat("*Click and hover on points in the plot below to explore enriched pathways.*\n\n")

print(htmltools::tags$iframe(
src = plot_path,
width = "100%",
height = "600px",
scrolling = "auto",
frameBorder = 0
))

cat("\n\n")
} else {
cat("No interactive plot available for this contrast.\n\n")
}
# Check and include interactive table
if (!file.exists(table_path) || file.size(table_path) == 0){
cat(paste0("No ", ifelse(params$gprofiler2_significant, "significantly", ""), " enriched pathways were found for this contrast."))
} else {
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