From 5e276a4ec372c2b6fd2b0b6b1161a3d644fc05a3 Mon Sep 17 00:00:00 2001 From: Dylan Jay Date: Mon, 28 Aug 2023 17:04:58 +0700 Subject: [PATCH] Centaurus variant group --- covid_plot_tests.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/covid_plot_tests.py b/covid_plot_tests.py index 07785e33..a589aecb 100644 --- a/covid_plot_tests.py +++ b/covid_plot_tests.py @@ -72,14 +72,14 @@ "ED.": "BA.4/BA.5 (Omicron)", "EZ.": "BA.4/BA.5 (Omicron)", "FM.": "BA.4/BA.5 (Omicron)", - "BA.2.75": "BA.2.75/BN.1/CH.1 (Omicron)", - "BA.2.76": "BA.2.75/BN.1/CH.1 (Omicron)", - "BN.": "BA.2.75/BN.1/CH.1 (Omicron)", - "CH.": "BA.2.75/BN.1/CH.1 (Omicron)", - "BR.": "BA.2.75/BN.1/CH.1 (Omicron)", - "FK.": "BA.2.75/BN.1/CH.1 (Omicron)", - "DV.": "BA.2.75/BN.1/CH.1 (Omicron)", - "EJ.": "BA.2.75/BN.1/CH.1 (Omicron)", + "BA.2.75": "BA.2.75/BN.1/CH.1 (Centaurus)", + "BA.2.76": "BA.2.75/BN.1/CH.1 (Centaurus)", + "BN.": "BA.2.75/BN.1/CH.1 (Centaurus)", + "CH.": "BA.2.75/BN.1/CH.1 (Centaurus)", + "BR.": "BA.2.75/BN.1/CH.1 (Centaurus)", + "FK.": "BA.2.75/BN.1/CH.1 (Centaurus)", + "DV.": "BA.2.75/BN.1/CH.1 (Centaurus)", + "EJ.": "BA.2.75/BN.1/CH.1 (Centaurus)", "FY.": "XBB (Arcturus)", # see https://github.com/MurrellGroup/lineages "FU.": "XBB (Arcturus)", "EQ.": "XBB (Arcturus)", @@ -177,7 +177,7 @@ def save_variant_plots(df: pd.DataFrame) -> None: variants = variants.reindex(pd.date_range(df.index.min(), df.index.max(), freq='D')).interpolate() footnote = "Estimate of variants in {} based on random sampling\nof Case PCR Genetic sequencing submitted to GISAID." - cols = rearrange(variants.columns.to_list(), "BA.2.75/BN.1/CH.1 (Omicron)", + cols = rearrange(variants.columns.to_list(), "BA.2.75/BN.1/CH.1 (Centaurus)", "XBB (Arcturus)", "EG (Eris)", "Other", first=False) variants['Cases'] = df['Cases'] case_variants = (variants[cols].multiply(variants['Cases'], axis=0)).dropna(axis=0, how="all")