src/07_ribosome_density.py: changes to display only ribosome density for one treatment at a time

src/07_ribosome_density.py

@@ -23,8 +23,10 @@ class Config_file:
     htseq_rnaseq = htseq_fold / "htseq_count_rna"
     htseq_ribo = htseq_fold / "htseq_count_ribo"
     result = Path(__file__).parents[1] / "results"
-    tdd_braf = result / "TDD_analysis" / "correlation" / "TDD_BRAF.txt"
-    tdd_dmso = result / "TDD_analysis" / "correlation" / "TDD_DMSO.txt"
+    tdd_braf_itdd = result / "TDD_analysis" / "correlation" / \
+        "TDD_BRAF_BRAF_DOWN.txt"
+    tdd_dmso_dtdd = result / "TDD_analysis" / "correlation" / \
+        "TDD_DMSO_BRAF_UP.txt"
     output = result / "TDD_analysis" / "density_figures"
 
 
@@ -35,7 +37,7 @@ def load_htseqfiles(mfolder: Path) -> List[Path]:
     :param mfolder: A folder containing htseq count file
     :return: The list of files in `mfolder`
 
-    >>> res = load_htseqfiles(Config_file.htseq_ribo)
+    >>> res = lrgoad_htseqfiles(Config_file.htseq_ribo)
     >>> len(res)
     6
     >>> [x.stem for x in res[0:2]]
@@ -203,10 +205,9 @@ def avg_replicate(df_density: pd.DataFrame) -> pd.DataFrame:
     3    D      DMSO  CTRL  2.125000
     4    E      DMSO  CTRL  2.600000
     """
-    df = df_density.drop("replicate", axis=1) \
-        .groupby(["gene", "treatment", "group"]) \
-        .mean().reset_index()
-    return df
+    return df_density.drop(
+        "replicate", axis=1).groupby(
+        ["gene", "treatment", "group"]).mean().reset_index()
 
 
 def statistical_analysis(df_density: pd.DataFrame, output: Path,
@@ -225,7 +226,7 @@ def statistical_analysis(df_density: pd.DataFrame, output: Path,
     treat = df_density["treatment"].unique()[0]
     outfig = output / f"diag_{treat}_{list_type}.pdf"
     outpval = output / f"diag_pval_{treat}_{list_type}.txt"
-    stat_s = r(f"""
+    stat_s = r("""
     require("DHARMa")
     require("glmmTMB")
     function(data, outfig, outpval){{
@@ -257,32 +258,35 @@ def create_density_figure(df_density: pd.DataFrame, gene_file: Path,
     df_density dataframe
     :param output_file: File where the figure will be created
     """
-    sns.set(context="talk")
+    sns.set_theme(context="talk", font_scale=2, style="whitegrid")
     df_mean = avg_replicate(df_density)
     df_mean["log10_density"] = np.log(df_mean["density"] + 1)
-    g = sns.catplot(x="treatment", y="log10_density", hue="group",
-                    data=df_mean, kind="violin", height=10, aspect=1.7,
-                    palette={"TDD_BRAF": "#a600ff", "CTRL": "dimgrey",
-                             "TDD_DMSO": "#ff8400"}, cut=True)
-    pdmso = statistical_analysis(
-        df_density[df_density["treatment"] == "DMSO"].copy(),
-        output_file.parent, gene_file.stem)
-    pbraf = statistical_analysis(
-        df_density[df_density["treatment"] == "BRAF"].copy(),
+    ctreatment = "DMSO" if "UP" in gene_file.stem else "BRAF"
+    df_mean = df_mean[df_mean["treatment"] == ctreatment]
+    pval = statistical_analysis(
+        df_density[df_density["treatment"] == ctreatment].copy(),
         output_file.parent, gene_file.stem)
-    pdmso = "%.2e" % pdmso
-    pbraf = "%.2e" % pbraf
-    g.fig.suptitle(f"Ribosome density "
-                   f"between {gene_file.stem} and CTRL"
-                   f"genes in BRAF and DMSO condition\n"
-                   f"(p_treatment_BRAF = {pbraf} & p_treatment_DMSO = {pdmso}")
-    g.set(ylabel="log10(density +1)")
+    g = sns.catplot(x="group", y="log10_density",
+                    data=df_mean, kind="violin", height=10, aspect=1.7,
+                    palette={"TDD_BRAF_BRAF_DOWN": "grey", "CTRL": "white",
+                             "TDD_DMSO_BRAF_UP": "grey"}, cut=True)
+    pval = "%.2e" % pval
+    title = f"Ribosome density " \
+            f"between {gene_file.stem} and CTRL" \
+            f"genes in {ctreatment} condition\n" \
+            f"(pval = {pval})"
+    g.fig.subplots_adjust(top=0.98)
+    g.fig.suptitle(title, fontsize=10)
+    g.set(ylabel="log10(density +1)", xlabel="")
     g.savefig(output_file)
 
 
 def density_figure_maker():
+    """
+    Create the violin indicating the ribosome density figure
+    """
     df = create_density_df()
-    list_files = [Config_file.tdd_braf, Config_file.tdd_dmso]
+    list_files = [Config_file.tdd_braf_itdd, Config_file.tdd_dmso_dtdd]
     for mfile in list_files:
         dfc = add_group_column(df.copy(), mfile)
         Config_file.output.mkdir(exist_ok=True)