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Add fc_threshold parameter to cnetplot #338

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Add fc_threshold parameter to cnetplot #338

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17ae657
Add fc_threshold parameter to cnetplot for filtering genes by fold ch…
ivokwee Nov 21, 2025
3385c7e
Merge pull request #3 from ivokwee/cnetplot-addthreshold
ivokwee Nov 22, 2025
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13 changes: 13 additions & 0 deletions R/cnetplot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
#' @param size_edge relative size of edge
#' @param node_label one of 'all', 'none', 'category', 'item', 'exclusive' or 'share'
#' @param foldChange numeric values to color the item (e.g, foldChange of gene expression values)
#' @param fc_threshold threshold for filtering genes by absolute fold change (e.g., fc_threshold = 1 keeps only genes with |foldChange| > 1)
#' @param hilight selected category to be highlighted
#' @param hilight_alpha transparent value for not selected to be highlight
#' @param ... additional parameters
Expand All @@ -33,13 +34,25 @@ cnetplot.enrichResult <- function(
size_edge = .5,
node_label = "all",
foldChange = NULL,
fc_threshold = NULL,
hilight = "none",
hilight_alpha = .3,
...
) {
geneSets <- extract_geneSets(x, showCategory)
foldChange <- fc_readable(x, foldChange)

# Filter genes by absolute fold change threshold
if (!is.null(fc_threshold) && !is.null(foldChange)) {
keep_genes <- names(foldChange)[abs(foldChange) > fc_threshold]
foldChange <- foldChange[keep_genes]
geneSets <- lapply(geneSets, function(gs) {
intersect(gs, keep_genes)
})
# Remove empty gene sets
geneSets <- geneSets[sapply(geneSets, length) > 0]
}

p <- cnetplot(
geneSets,
layout = layout,
Expand Down