refactor: Refactor meta comparison (#114)

This PR does some minor refactoring in the meta comparison code as they were still some comments from @dlaehnemann in #113 that havent been addressed.
snakemake-workflows · Sep 11, 2024 · 5bf9ea0 · 5bf9ea0
1 parent 3f8f126
commit 5bf9ea0
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Showing 3 changed files with 11 additions and 12 deletions.
diff --git a/workflow/scripts/compare_diffexp.py b/workflow/scripts/compare_diffexp.py
@@ -5,8 +5,8 @@
 
 diffexp_x = pl.from_pandas(pyreadr.read_r(snakemake.input[0])[None]).lazy()
 diffexp_y = pl.from_pandas(pyreadr.read_r(snakemake.input[1])[None]).lazy()
-label_x = list(snakemake.params.labels.keys())[0]
-label_y = list(snakemake.params.labels.keys())[1]
+label_x = list(snakemake.params.labels)[0]
+label_y = list(snakemake.params.labels)[1]
 
 effect_x = f"effect {label_x} (beta score)"
 effect_y = f"effect {label_y} (beta score)"

diff --git a/workflow/scripts/compare_enrichment.py b/workflow/scripts/compare_enrichment.py
@@ -4,8 +4,8 @@
 
 diffexp_x = pl.read_csv(snakemake.input[0], separator="\t").lazy()
 diffexp_y = pl.read_csv(snakemake.input[1], separator="\t").lazy()
-label_x = list(snakemake.params.labels.keys())[0]
-label_y = list(snakemake.params.labels.keys())[1]
+label_x = list(snakemake.params.labels)[0]
+label_y = list(snakemake.params.labels)[1]
 
 effect_x_pos = f"positive effect {label_x}"
 effect_y_pos = f"positive effect {label_y}"
@@ -37,10 +37,9 @@ def prepare(df):
     # Select necessary columns
     df = (
         df.select(
-            [cs.by_name("GO", "term", "p_uncorrected", "p_fdr_bh", "study_items")]
+            cs.by_name("GO", "term", "p_uncorrected", "p_fdr_bh", "study_items")
         )
         .with_columns(
-            [
                 pl.col("study_items")
                 .map_elements(
                     extract_study_items,
@@ -51,7 +50,6 @@ def prepare(df):
                     ),
                 )
                 .alias("parsed_terms")
-            ]
         )
         .with_columns(
             [
@@ -102,7 +100,8 @@ def plot(df, effect_x, effect_y, title, xlabel, ylabel):
     line = (
         alt.Chart(
             pl.DataFrame(
-                {effect_x: [min_value, max_value], effect_y: [min_value, max_value]}
+                {effect_x: [min_value, max_value], effect_y: [min_value, max_value]},
+                schema={effect_x: pl.Float64, effect_y: pl.Float64},
             )
         )
         .mark_line(color="lightgrey")

diff --git a/workflow/scripts/compare_pathways.py b/workflow/scripts/compare_pathways.py
@@ -4,8 +4,8 @@
 
 diffexp_x = pl.read_csv(snakemake.input[0], separator="\t").lazy()
 diffexp_y = pl.read_csv(snakemake.input[1], separator="\t").lazy()
-label_x = list(snakemake.params.labels.keys())[0]
-label_y = list(snakemake.params.labels.keys())[1]
+label_x = list(snakemake.params.labels)[0]
+label_y = list(snakemake.params.labels)[1]
 
 
 effect_x = f"effect {label_x}"
@@ -106,8 +106,8 @@ def prepare(df):
     )
 )
 
-min_value = combined.select(pl.min(effect_x, effect_y)).min_horizontal()[0]
-max_value = combined.select(pl.max(effect_x, effect_y)).max_horizontal()[0]
+min_value = min(df[effect_x].min(), df[effect_y].min())
+max_value = max(df[effect_x].max(), df[effect_y].max())
 
 line = (
     alt.Chart(