From 1a3480cc692c1d7b7042b2bb0d0175f4b298e880 Mon Sep 17 00:00:00 2001
From: Sigve Nakken <sigven@ifi.uio.no>
Date: Wed, 31 Jul 2024 21:29:16 +0200
Subject: [PATCH] fix tumor purity/ploidy display

---
 pcgr/config.py                                       |  4 ++--
 pcgrr/inst/templates/pcgr_quarto_report/settings.qmd | 12 ++++++------
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/pcgr/config.py b/pcgr/config.py
index 10b2ec57..486de4bb 100644
--- a/pcgr/config.py
+++ b/pcgr/config.py
@@ -44,8 +44,8 @@ def create_config(arg_dict, workflow = "PCGR"):
         
     if workflow == 'PCGR':
         conf_options['assay_properties'] = {}
-        conf_options['sample_properties']['purity'] = 'NA'
-        conf_options['sample_properties']['ploidy'] = 'NA'
+        conf_options['sample_properties']['tumor_purity'] = 'NA'
+        conf_options['sample_properties']['tumor_ploidy'] = 'NA'
         conf_options['sample_properties']['site'] = str(pcgr_vars.tsites[arg_dict['tsite']])
         conf_options['sample_properties']['site2'] = str(pcgr_vars.tsites[arg_dict['tsite']]).replace(" ","_").replace("/","@")
         conf_options['sample_properties']['dp_control_detected'] = 0
diff --git a/pcgrr/inst/templates/pcgr_quarto_report/settings.qmd b/pcgrr/inst/templates/pcgr_quarto_report/settings.qmd
index 641a4b4b..eea562f0 100644
--- a/pcgrr/inst/templates/pcgr_quarto_report/settings.qmd
+++ b/pcgrr/inst/templates/pcgr_quarto_report/settings.qmd
@@ -15,14 +15,14 @@ assay_type <- conf$assay_properties$type
 tumor_site <- conf$sample_properties$site
 assay_mode <- conf$assay_properties$mode
 tumor_ploidy <- "N/A"
-if(!is.na(conf$sample_properties$ploidy) &
-   conf$sample_properties$ploidy != "NA"){
-  tumor_ploidy <- conf$sample_properties$ploidy
+if(!is.na(conf$sample_properties$tumor_ploidy) &
+   conf$sample_properties$tumor_ploidy != "NA"){
+  tumor_ploidy <- conf$sample_properties$tumor_ploidy
 }
 tumor_purity <- "N/A"
-if(!is.na(conf$sample_properties$purity) &
-   conf$sample_properties$purity != "NA"){
-  tumor_purity <- conf$sample_properties$purity
+if(!is.na(conf$sample_properties$tumor_purity) &
+   conf$sample_properties$tumor_purity != "NA"){
+  tumor_purity <- conf$sample_properties$tumor_purity
 }
 
 target_size <- conf$assay_properties$effective_target_size_mb