From dbedd94bdcd004f6005411e345af9f23904dcb8b Mon Sep 17 00:00:00 2001
From: Marcus Fedarko <mfedarko@ucsd.edu>
Date: Wed, 20 Feb 2019 20:45:09 -0800
Subject: [PATCH] RM use of sample ranks variable from most of code

Since it wasn't getting used for anything after matching it with the
BIOM table's dataframe.

See #46 for a relevant discussion.
---
 rankratioviz/generate.py      | 9 ++++-----
 rankratioviz/q2/_method.py    | 4 ++--
 rankratioviz/scripts/_plot.py | 4 ++--
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/rankratioviz/generate.py b/rankratioviz/generate.py
index 512b552d..b8dfa200 100755
--- a/rankratioviz/generate.py
+++ b/rankratioviz/generate.py
@@ -71,15 +71,14 @@ def process_input(ordination_file, biom_table, taxam=None):
                 V.index = matched_taxam["Taxon"].values
                 table.columns = matched_taxam["Taxon"].values
 
-    return U, V, table
+    return V, table
 
 
-def gen_rank_plot(U, V, rank_col):
+def gen_rank_plot(V, rank_col):
     """Generates altair.Chart object describing the rank plot.
 
     Arguments:
 
-    U: sample ranks
     V: feature ranks
     rank_col: the column index to use for getting the rank values from a taxon.
 
@@ -222,7 +221,7 @@ def gen_sample_plot(table, metadata, category, palette='Set1'):
     return sample_logratio_chart_json
 
 
-def gen_visualization(U, V, processed_table, df_sample_metadata, category,
+def gen_visualization(V, processed_table, df_sample_metadata, category,
                       output_dir):
     """Creates a rankratioviz visualization. This function should be callable
        from both the QIIME 2 and standalone rankratioviz scripts.
@@ -232,7 +231,7 @@ def gen_visualization(U, V, processed_table, df_sample_metadata, category,
        index_path: a path to the index.html file for the output visualization.
                    This is needed when calling q2templates.render().
     """
-    rank_plot_chart = gen_rank_plot(U, V, 0)
+    rank_plot_chart = gen_rank_plot(V, 0)
     sample_plot_json = gen_sample_plot(processed_table, df_sample_metadata,
                                        category)
     os.makedirs(output_dir, exist_ok=True)
diff --git a/rankratioviz/q2/_method.py b/rankratioviz/q2/_method.py
index ca1e6359..a97847bb 100644
--- a/rankratioviz/q2/_method.py
+++ b/rankratioviz/q2/_method.py
@@ -23,11 +23,11 @@ def plot(output_dir: str, ranks: skbio.OrdinationResults, table: biom.Table,
     """
     # get data
     df_feature_metadata = feature_metadata.to_dataframe()
-    U, V, processed_table = process_input(ranks, table, df_feature_metadata)
+    V, processed_table = process_input(ranks, table, df_feature_metadata)
     # We can't "subscript" Q2 Metadata types, so we have to convert this to a
     # dataframe before working with it
     df_sample_metadata = sample_metadata.to_dataframe()
-    index_path = gen_visualization(U, V, processed_table, df_sample_metadata,
+    index_path = gen_visualization(V, processed_table, df_sample_metadata,
                                    category, output_dir)
     # render the visualization using q2templates.render().
     # TODO: do we need to specify plot_name in the context in this way? I'm not
diff --git a/rankratioviz/scripts/_plot.py b/rankratioviz/scripts/_plot.py
index 1b5c0709..4d83826e 100644
--- a/rankratioviz/scripts/_plot.py
+++ b/rankratioviz/scripts/_plot.py
@@ -39,8 +39,8 @@ def plot(ranks: str, table: str, sample_metadata: str, feature_metadata: str,
         taxonomy = pd.read_csv(feature_metadata, sep='\t')
         taxonomy.set_index('feature id', inplace=True)
 
-    U, V, processed_table = process_input(ranks, loaded_biom, taxonomy)
-    gen_visualization(U, V, processed_table, df_sample_metadata, category,
+    V, processed_table = process_input(ranks, loaded_biom, taxonomy)
+    gen_visualization(V, processed_table, df_sample_metadata, category,
                       output_dir)