From 9c08d3a95cca5bf503353f5c6b824f4dbb857a41 Mon Sep 17 00:00:00 2001
From: Adrian Salavaty <abbas.salavaty@gmail.com>
Date: Thu, 9 Nov 2023 11:58:47 +1100
Subject: [PATCH] Debug exir function.

---
 R/functions.R             | 6 +++++-
 inst/ShinyApps/ExIR/app.R | 6 +++++-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/R/functions.R b/R/functions.R
index 7235b45..19b60a5 100755
--- a/R/functions.R
+++ b/R/functions.R
@@ -2407,7 +2407,11 @@ sirir <- function(graph, vertices = V(graph),
         rf.diff.exptl.pvalue <- base::subset(rf.diff.exptl.pvalue, rf.diff.exptl.pvalue$pvalue < alpha)
 
       } else {
-        rf.pval.select <- which(rf.diff.exptl.pvalue[,"pvalue"] <alpha)
+        if(length(which(rf.diff.exptl.pvalue[, "pvalue"] < alpha)) >= 10) {
+          rf.pval.select <- which(rf.diff.exptl.pvalue[, "pvalue"] < alpha)
+        } else {
+          rf.pval.select <- which(order(rf.diff.exptl.pvalue[, "pvalue"]) <= 10)
+        }
         rf.nonSig <- seq(nrow(rf.diff.exptl.pvalue))[-rf.pval.select]
         required.pos.importance <- select.number - length(rf.pval.select)
 
diff --git a/inst/ShinyApps/ExIR/app.R b/inst/ShinyApps/ExIR/app.R
index cc999ca..e924364 100755
--- a/inst/ShinyApps/ExIR/app.R
+++ b/inst/ShinyApps/ExIR/app.R
@@ -2328,7 +2328,11 @@ server <- function(input, output, session,
             rf.diff.exptl.pvalue <- base::subset(rf.diff.exptl.pvalue, rf.diff.exptl.pvalue$pvalue < alpha)
 
         } else {
-            rf.pval.select <- which(rf.diff.exptl.pvalue[,"pvalue"] <alpha)
+          if(length(which(rf.diff.exptl.pvalue[, "pvalue"] < alpha)) >= 10) {
+            rf.pval.select <- which(rf.diff.exptl.pvalue[, "pvalue"] < alpha)
+          } else {
+            rf.pval.select <- which(order(rf.diff.exptl.pvalue[, "pvalue"]) <= 10)
+          }
             rf.nonSig <- seq(nrow(rf.diff.exptl.pvalue))[-rf.pval.select]
             required.pos.importance <- select.number - length(rf.pval.select)