feat(getSubnetworkFromIndra): Add filter for including infinity fold change

R/getSubnetworkFromIndra.R

@@ -35,6 +35,12 @@
 #' @param filter_by_ptm_site logical, whether to filter edges based on whether the 
 #' site information from INDRA matches with the PTM site in the input.  Default is FALSE.  
 #' Only applicable for differential PTM abundance results.
+#' @param include_infinite_fc logical, whether to include proteins with 
+#' infinite log fold change (i.e. proteins that are only detected in one condition).  
+#' Default is FALSE.
+#' @param direction Character string specifying the direction of regulation to
+#' include. One of \code{"both"} (default), \code{"up"} (upregulated only),
+#' or \code{"down"} (downregulated only).
 #'
 #' @return list of 2 data.frames, nodes and edges
 #'
@@ -60,8 +66,11 @@ getSubnetworkFromIndra <- function(input,
                                    logfc_cutoff = NULL,
                                    force_include_other = NULL, 
                                    filter_by_curation = FALSE,
-                                   filter_by_ptm_site = FALSE) {
-    input <- .filterGetSubnetworkFromIndraInput(input, pvalueCutoff, logfc_cutoff, force_include_other)
+                                   filter_by_ptm_site = FALSE,
+                                   include_infinite_fc = FALSE,
+                                   direction = c("both", "up", "down")) {
+    direction = match.arg(direction)
+    input <- .filterGetSubnetworkFromIndraInput(input, pvalueCutoff, logfc_cutoff, force_include_other, include_infinite_fc, direction)
     .validateGetSubnetworkFromIndraInput(input, protein_level_data, sources_filter, force_include_other)
     res <- .callIndraCogexApi(input$HgncId, force_include_other)
     res <- .filterIndraResponse(res, statement_types, evidence_count_cutoff, sources_filter)

R/utils_cytoscapeNetwork.R

@@ -10,9 +10,17 @@
         return(rep("#D3D3D3", length(logFC_values)))
     }
 
+    is_pos_inf <- is.infinite(logFC_values) & logFC_values > 0
+    is_neg_inf <- is.infinite(logFC_values) & logFC_values < 0
+
+    finite_values   <- logFC_values[is.finite(logFC_values)]
     default_max     <- 2
-    max_logFC       <- max(c(abs(logFC_values), default_max), na.rm = TRUE)
+    max_logFC       <- max(c(abs(finite_values), default_max), na.rm = TRUE)
     min_logFC       <- -max_logFC
+
+    logFC_values[is_pos_inf] <-  max_logFC
+    logFC_values[is_neg_inf] <-  min_logFC
+
     color_map       <- grDevices::colorRamp(colors)
     normalized      <- (logFC_values - min_logFC) / (max_logFC - min_logFC)
     normalized[is.na(normalized)] <- 0.5

R/utils_getSubnetworkFromIndra.R

@@ -132,10 +132,21 @@
 #' @param pvalueCutoff p-value cutoff
 #' @param logfc_cutoff logFC cutoff
 #' @param force_include_other list of identifiers to exempt from filtering
+#' @param include_infinite_fc logical, whether to include proteins with 
+#' infinite log fold change (i.e. proteins that are only detected in one condition).  
+#' Default is FALSE. 
+#' @param direction Character string specifying the direction of regulation to
+#' include. One of \code{"both"} (default), \code{"up"} (upregulated only),
+#' or \code{"down"} (downregulated only).
 #' @return filtered groupComparison result
 #' @keywords internal
 #' @noRd
-.filterGetSubnetworkFromIndraInput <- function(input, pvalueCutoff, logfc_cutoff, force_include_other) {
+.filterGetSubnetworkFromIndraInput <- function(input, 
+                                               pvalueCutoff, 
+                                               logfc_cutoff, 
+                                               force_include_other, 
+                                               include_infinite_fc, 
+                                               direction) {
     input$Protein <- as.character(input$Protein)
 
     # Extract exempt proteins before any filtering
@@ -152,7 +163,11 @@
         }
     }
 
-    # Apply standard filtering
+    infinite_fc_proteins <- NULL
+    if (include_infinite_fc) {
+        infinite_fc_proteins <- input[is.infinite(input$log2FC), ]
+    }
+
     input <- input[!is.na(input$adj.pvalue),]
     if (!is.null(pvalueCutoff)) {
         input <- input[input$adj.pvalue < pvalueCutoff, ]
@@ -163,8 +178,16 @@
         }
         input <- input[!is.na(input$log2FC) & abs(input$log2FC) > logfc_cutoff, ]
     }
-    if ("issue" %in% colnames(input)) {
-        input <- input[is.na(input$issue), ]
+
+    if (!is.null(infinite_fc_proteins) && nrow(infinite_fc_proteins) > 0) {
+        combined_input <- rbind(infinite_fc_proteins, input)
+        input <- combined_input[!duplicated(combined_input$Protein), ]
+    }
+
+    if (direction == "up") {
+        input <- input[!is.na(input$log2FC) & input$log2FC > 0, ]
+    } else if (direction == "down") {
+        input <- input[!is.na(input$log2FC) & input$log2FC < 0, ]
     }
 
     # Combine filtered data with exempt proteins and remove duplicates
@@ -186,6 +209,7 @@
     }
     return(input)
 }
+
 #' Add additional metadata to an edge
 #' @param edge object representation of an INDRA statement
 #' @param input filtered groupComparison result

tests/testthat/test-utils_cytoscapeNetwork.R

@@ -69,6 +69,12 @@ test_that(".mapLogFCToColor handles empty input", {
     expect_length(colors, 0)
 })
 
+test_that(".mapLogFCToColor handles Inf and -Inf values", {
+    colors <- MSstatsBioNet:::.mapLogFCToColor(c(-Inf, 0, Inf))
+    expect_length(colors, 3)
+    expect_true(all(grepl("^#[0-9A-Fa-f]{6}$", colors)))
+})
+
 # =============================================================================
 # .relProps
 # =============================================================================