From 63e0fe6524b70ed81d95ac6cbf05c390fcbc506b Mon Sep 17 00:00:00 2001
From: Sarah Griffiths <sarah.griffiths@nanoporetech.com>
Date: Wed, 10 Apr 2024 08:09:23 +0000
Subject: [PATCH] change significance level to mark on MA plot

---
 CHANGELOG.md      |  4 ++++
 bin/de_analysis.R | 13 ++++++++++++-
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f46e5e6..1a0e3b8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [unreleased]
+### Changed
+- MA plot in the `results_dge.pdf` has been updated to match the MA plot in the report.
+
 ## [v1.1.1]
 ### Changed
 - Improved handling of different annotation file types (eg. `.gtf/.gff/.gff3`) in `de_analysis` mode.
diff --git a/bin/de_analysis.R b/bin/de_analysis.R
index 4aae056..b76c106 100755
--- a/bin/de_analysis.R
+++ b/bin/de_analysis.R
@@ -123,7 +123,18 @@ qlf <- glmQLFTest(fit)
 edger_res <- topTags(qlf, n=nrow(y), sort.by="PValue")[[1]]
 
 pdf("de_analysis/results_dge.pdf")
-plotMD(qlf)
+
+# create status vector
+status <- ifelse(
+  qlf$PValue<0.01 & qlf$logFC>0, 
+  'up', 
+  ifelse(
+    qlf$PValue<0.01 & qlf$logFC<=0,
+    'down',
+    'notsig'
+  )
+)
+plotMD(qlf, status=status,  values=c("up","down","notsig"), hl.col=c("red","blue","black"))
 abline(h=c(-1,1), col="blue")
 plotQLDisp(fit)