From 5f3a40c35adbea37b669228ef955057ee7ac29a1 Mon Sep 17 00:00:00 2001
From: Antonietta Salerno <62121166+antosalerno@users.noreply.github.com>
Date: Wed, 25 Sep 2024 11:13:06 +0200
Subject: [PATCH] fix volcano

---
 N01_GeoMx_Enrich.R | 0
 S08_CopperJoint.R  | 1 -
 S10_Neutrophils.R  | 0
 session_info.txt   | 0
 supportFunctions.R | 2 +-
 5 files changed, 1 insertion(+), 2 deletions(-)
 mode change 100644 => 100755 N01_GeoMx_Enrich.R
 mode change 100644 => 100755 S10_Neutrophils.R
 mode change 100644 => 100755 session_info.txt

diff --git a/N01_GeoMx_Enrich.R b/N01_GeoMx_Enrich.R
old mode 100644
new mode 100755
diff --git a/S08_CopperJoint.R b/S08_CopperJoint.R
index a357880..114c424 100755
--- a/S08_CopperJoint.R
+++ b/S08_CopperJoint.R
@@ -164,4 +164,3 @@ dev.off()
 
 
 
-
diff --git a/S10_Neutrophils.R b/S10_Neutrophils.R
old mode 100644
new mode 100755
diff --git a/session_info.txt b/session_info.txt
old mode 100644
new mode 100755
diff --git a/supportFunctions.R b/supportFunctions.R
index 98f2d1c..442af8b 100755
--- a/supportFunctions.R
+++ b/supportFunctions.R
@@ -104,7 +104,7 @@ plotVolcano <- function(clusters, res=NULL, type = "condition", file= NULL,
                          drawConnectors = TRUE,
                          widthConnectors = 0.3,colConnectors = 'gray51', maxoverlapsConnectors = Inf,
                          caption = paste0('Upregulated = ', nrow(res[res$avg_log2FC > log2FC&res$p_val_adj<= 0.05,]), ' genes',
-                                          "\n",'Downregulated = ', nrow(res[res$avg_log2FC < -log2FC &res$p_val_adj<= 0.05,]), ' genes'))+ theme(plot.title = element_text(hjust = 0.5)) + coord_flip()
+                                          "\n",'Downregulated = ', nrow(res[res$avg_log2FC < -log2FC &res$p_val_adj<= 0.05,]), ' genes'))+ theme(plot.title = element_text(hjust = 0.5))
       ggsave(p, file=paste0("TEPA_plots/",save, "DEA_",sub(" ", "_", cluster),".png"), width = 30, height = 25, units = "cm")
     })
   }