From 733367d2b99b7176f6f20d35bcac2ba8c2cf6feb Mon Sep 17 00:00:00 2001
From: simonleandergrimm <simonleandergrimm@gmail.com>
Date: Wed, 10 Jul 2024 11:02:02 -0400
Subject: [PATCH] Edited clade-count-comparison.py. Adapted comp-fig-1 script
 to use human_clade_counts_new.tsv (will have to fix that in future.)#FIXME.

---
 figures/clade-count-comparison.py | 34 +++++++++++++++----------------
 figures/composite_fig_1.py        |  4 ++--
 2 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/figures/clade-count-comparison.py b/figures/clade-count-comparison.py
index 6969e97..eef8206 100644
--- a/figures/clade-count-comparison.py
+++ b/figures/clade-count-comparison.py
@@ -11,23 +11,23 @@
 
 
 TARGET_STUDY_METADATA = {
-    "Bengtsson-Palme 2016": ["PRJEB14051"],
-    "Munk 2022": [
-        "PRJEB13831",
-        "PRJEB27054",
-        "PRJEB27621",
-        "PRJEB40798",
-        "PRJEB40815",
-        "PRJEB40816",
-        "PRJEB51229",
-    ],
-    "Brinch 2020": ["PRJEB13832", "PRJEB34633"],
-    "Ng 2019": ["PRJNA438174"],
-    "Maritz 2019": ["PRJEB28033"],
-    "Brumfield 2022": ["PRJNA812772"],
-    "Yang 2020": ["PRJNA645711"],
-    "Spurbeck 2023": ["PRJNA924011"],
-    "CC 2021": ["PRJNA661613"],
+    # "Bengtsson-Palme 2016": ["PRJEB14051"],
+    # "Munk 2022": [
+    #     "PRJEB13831",
+    #     "PRJEB27054",
+    #     "PRJEB27621",
+    #     "PRJEB40798",
+    #     "PRJEB40815",
+    #     "PRJEB40816",
+    #     "PRJEB51229",
+    # ],
+    # "Brinch 2020": ["PRJEB13832", "PRJEB34633"],
+    # "Ng 2019": ["PRJNA438174"],
+    # "Maritz 2019": ["PRJEB28033"],
+    # "Brumfield 2022": ["PRJNA812772"],
+    # "Yang 2020": ["PRJNA645711"],
+    # "Spurbeck 2023": ["PRJNA924011"],
+    # "CC 2021": ["PRJNA661613"],
     "Rothman 2021": ["PRJNA729801"],
 }
 
diff --git a/figures/composite_fig_1.py b/figures/composite_fig_1.py
index 192491f..7a6e896 100644
--- a/figures/composite_fig_1.py
+++ b/figures/composite_fig_1.py
@@ -51,7 +51,7 @@
 
 sample_files = [
     "taxonomic_composition",
-    "hv_clade_counts",
+    "hv_clade_counts_new",  # FIXME
     "kraken_reports",
     "qc_basic_stats",
     "sample-metadata",
@@ -146,7 +146,7 @@ def assemble_plotting_dfs() -> tuple[pd.DataFrame, pd.DataFrame]:
             }
 
             hv_clade_counts = pd.read_csv(
-                f"../{BIOPROJECT_DIR}/{study_bioproject}/hv_clade_counts.tsv",
+                f"../{BIOPROJECT_DIR}/{study_bioproject}/hv_clade_counts_new.tsv",
                 sep="\t",
             )