From ac4a73b5a4102f96aeb18edc7df523446ef35533 Mon Sep 17 00:00:00 2001
From: Addimator <44083468+Addimator@users.noreply.github.com>
Date: Fri, 20 Sep 2024 10:33:27 +0200
Subject: [PATCH] fix: Move signed_pi_value columns to the end (again) (#117)

- Undo my overwriting of the position of the signed_pi_cols
- Small bug fixes

---------

Co-authored-by: Addimator <adpri100hhu.de>
---
 .../resources/datavzrd/diffexp-template.yaml  | 24 +++++++++++--------
 .../datavzrd/go-enrichment-template.yaml      |  2 +-
 .../resources/datavzrd/spia-template.yaml     |  7 ++++--
 workflow/scripts/compare_enrichment.py        |  2 +-
 workflow/scripts/compare_pathways.py          | 10 ++++----
 workflow/scripts/postprocess_diffexp.py       |  9 +++++--
 6 files changed, 33 insertions(+), 21 deletions(-)

diff --git a/workflow/resources/datavzrd/diffexp-template.yaml b/workflow/resources/datavzrd/diffexp-template.yaml
index fe82b179..04dab8e2 100644
--- a/workflow/resources/datavzrd/diffexp-template.yaml
+++ b/workflow/resources/datavzrd/diffexp-template.yaml
@@ -134,7 +134,7 @@ views:
           display-mode: hidden
         regex('qval_.+'):
           display-mode: hidden
-        regex('signed_pi_value_.+'):
+        ?f"regex('signed_pi_value_{params.primary_variable}.+')":
           display-mode: normal
           plot:
             heatmap:
@@ -147,8 +147,9 @@ views:
                 - -1
                 - 0
                 - 1
-        regex('^b_(?!.*_se$)'):
-          display-mode: normal
+        ?f"regex('signed_pi_value_(?!{params.primary_variable})')":
+          display-mode: hidden # Hide all signed pi cols that are not associated to the primary variable
+        ?f"regex('^b_(?!.*_se$)')":
           plot:
             heatmap:
               scale: linear
@@ -157,9 +158,9 @@ views:
                 - "white"
                 - "#6baed6"
               domain:
-                - -1
+                - -10
                 - 0
-                - 1
+                - 10
         regex('^b_.*_se$'):
           display-mode: hidden
         ?for sample in params.samples:
@@ -242,7 +243,7 @@ views:
           display-mode: hidden
         regex('qval_.+'):
           display-mode: hidden
-        regex('signed_pi_value_.+'):
+        ?f"regex('signed_pi_value_{params.primary_variable}.+')":
           display-mode: normal
           plot:
             heatmap:
@@ -255,8 +256,9 @@ views:
                 - -1
                 - 0
                 - 1
-        regex('b_.*(?<!_se(?!part2))'):
-          display-mode: normal
+        ?f"regex('signed_pi_value_(?!{params.primary_variable})')":
+          display-mode: hidden # Hide all signed pi cols that are not associated to the primary variable
+        ?f"regex('^b_(?!.*_se$)')":
           plot:
             heatmap:
               scale: linear
@@ -265,9 +267,11 @@ views:
                 - "white"
                 - "#6baed6"
               domain:
-                - -1
+                - -10
                 - 0
-                - 1
+                - 10
+        regex('^b_.*_se$'):
+          display-mode: hidden
         ?for sample in params.samples:
           ?sample:
             display-mode: hidden
diff --git a/workflow/resources/datavzrd/go-enrichment-template.yaml b/workflow/resources/datavzrd/go-enrichment-template.yaml
index 1469c3ae..9f2a83f2 100644
--- a/workflow/resources/datavzrd/go-enrichment-template.yaml
+++ b/workflow/resources/datavzrd/go-enrichment-template.yaml
@@ -52,7 +52,7 @@ views:
                 }
               }
             spec-path: ?input.vega_bars
-            vega-controls: true
+            vega-controls: false
         p_uncorrected:
           label: p-value
           plot:
diff --git a/workflow/resources/datavzrd/spia-template.yaml b/workflow/resources/datavzrd/spia-template.yaml
index 9e505ce2..653bd052 100644
--- a/workflow/resources/datavzrd/spia-template.yaml
+++ b/workflow/resources/datavzrd/spia-template.yaml
@@ -59,7 +59,7 @@ views:
                 }
               }
             spec-path: ?input.vega_circle
-            vega-controls: true
+            vega-controls: false
         p-value for at least NDE genes:
           display-mode: detail
         total perturbation accumulation:
@@ -70,7 +70,10 @@ views:
                 - "#B2182B"
                 - "#F7F7F7"
                 - "#2166AC"
-              domain-mid: 0
+              domain: 
+                - -100
+                - 0
+                - 100
         p-value to observe a total accumulation:
           display-mode: detail
         Combined p-value:
diff --git a/workflow/scripts/compare_enrichment.py b/workflow/scripts/compare_enrichment.py
index e1e70731..1be696a9 100644
--- a/workflow/scripts/compare_enrichment.py
+++ b/workflow/scripts/compare_enrichment.py
@@ -185,7 +185,7 @@ def plot(df, effect_x, effect_y, title, xlabel, ylabel):
         )
     )
 
-    point_selector = alt.selection_single(fields=["term"], empty="all")
+    point_selector = alt.selection_single(fields=["term"], empty=False)
     text_background = (
         alt.Chart(df)
         .mark_text(
diff --git a/workflow/scripts/compare_pathways.py b/workflow/scripts/compare_pathways.py
index 7ccdbe36..4f8601c2 100644
--- a/workflow/scripts/compare_pathways.py
+++ b/workflow/scripts/compare_pathways.py
@@ -82,7 +82,7 @@ def prepare(df):
 
 alt.data_transformers.disable_max_rows()
 points = (
-    alt.Chart(df)
+    alt.Chart(combined_pd)
     .mark_circle(size=15, tooltip={"content": "data"})
     .encode(
         alt.X(
@@ -102,8 +102,8 @@ def prepare(df):
     )
 )
 
-min_value = min(df[effect_x].min(), df[effect_y].min())
-max_value = max(df[effect_x].max(), df[effect_y].max())
+min_value = min(combined_pd[effect_x].min(), combined_pd[effect_y].min())
+max_value = max(combined_pd[effect_x].max(), combined_pd[effect_y].max())
 
 line = (
     alt.Chart(
@@ -140,7 +140,7 @@ def prepare(df):
 )
 
 text_background = (
-    alt.Chart(df)
+    alt.Chart(combined_pd)
     .mark_text(
         align="left",
         baseline="middle",
@@ -158,7 +158,7 @@ def prepare(df):
 )
 
 text = (
-    alt.Chart(df)
+    alt.Chart(combined_pd)
     .mark_text(
         align="left",
         baseline="middle",
diff --git a/workflow/scripts/postprocess_diffexp.py b/workflow/scripts/postprocess_diffexp.py
index c6e5c19e..da157f85 100644
--- a/workflow/scripts/postprocess_diffexp.py
+++ b/workflow/scripts/postprocess_diffexp.py
@@ -20,8 +20,13 @@ def sort_columns(df, matching_columns):
         for prefix in matching_columns
         for suffix in ["_lower", "", "_upper", "_se"]
     ]
-    other_columns = [col for col in df.columns if not col.startswith("b_")]
-    return df[other_columns + b_column_order]
+    signed_pi_columns = [col for col in df.columns if col.startswith("signed_pi_value")]
+    other_columns = [
+        col
+        for col in df.columns
+        if not col.startswith("b_") and not col.startswith("signed_pi_value")
+    ]
+    return df[other_columns + b_column_order + signed_pi_columns]
 
 
 def sort_rows(df):