Error model output

ci/recipe/meta.yaml

@@ -18,10 +18,13 @@ requirements:
 
   run:
     - python {{ python }}
+    - pandas {{ pandas }}
     - biom-format {{ biom_format }}
     - bioconductor-dada2
     - r-base {{ r_base }}
     - r-optparse >=1.7.1
+    - matplotlib >=3.8.4
+    - seaborn
     # openjdk is not a real dependency, but, r-base has a post-link and post-
     # activation hook that calls R CMD javareconf, which pokes around for any
     # installations of java. On modern versions of macOS, a binary called
@@ -32,11 +35,13 @@ requirements:
     - openjdk # [osx]
     - qiime2 {{ qiime2_epoch }}.*
     - q2-types {{ qiime2_epoch }}.*
+    - q2templates {{ qiime2_epoch }}.*
 
 test:
   requires:
     - qiime2 >={{ qiime2 }}
     - q2-types >={{ q2_types }}
+    - q2templates >={{ q2templates }}
     - pytest
 
   imports:

q2_dada2/_dada_stats/__init__.py

@@ -0,0 +1,11 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016-2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+from ._visualizer import stats_viz
+
+__all__ = ['stats_viz']

q2_dada2/_dada_stats/_visualizer.py

@@ -0,0 +1,147 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016-2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+import os
+import pkg_resources
+import shutil
+import matplotlib.pyplot as plt
+import seaborn as sns
+import qiime2.util
+import q2templates
+
+TEMPLATES = pkg_resources.resource_filename('q2_dada2._dada_stats', 'assets')
+
+
+def _plot_errors(transdf, image_paths_arr, output_dir,
+                 image_prefix, error_in, error_out, nominalq):
+
+    # generates baseline graph of obs errors
+    filtered_data = transdf[(transdf['from'].isin(["A", "C", "G", "T"])) &
+                            (transdf['to'].isin(["A", "C", "G", "T"]))]
+
+    g = sns.FacetGrid(filtered_data, col="Transition", col_wrap=4)
+    g.map(plt.scatter, "Qual", "Observed", color="gray")
+
+    # options for error graph; estimated line, nominal line, and input line
+    if error_out is True:
+        g.map(plt.plot, "Qual", "Estimated", color="gray")
+    if nominalq is True:
+        g.map(plt.plot, "Qual", "Nominal", color="red")
+    if error_in is True:
+        g.map(plt.plot, "Qual", "Input", color="blue")
+
+    # layout options to bring it into line with the dada2 ouput version
+    g.tight_layout()
+    g.set(yscale="log")
+    g.set_axis_labels("", "")
+    g.figure.text(0.5, 0.009, 'Consensus quality score',
+                  ha='center', va='center', fontsize=15)
+    g.figure.text(0.009, 0.5, 'Error frequency (log10)',
+                  ha='center', va='center', rotation='vertical', fontsize=15)
+
+    # save image for html rendering
+    for ext in ['png', 'svg']:
+        img_fp = os.path.join(output_dir,
+                              image_prefix + 'error_graph.%s' % ext)
+        if ext == 'png':
+            image_paths_arr.append(
+                './' + image_prefix + 'error_graph.png'
+            )
+        plt.savefig(img_fp)
+    plt.clf()
+    return image_paths_arr  # pass back path to image
+
+
+def stats_viz(output_dir: str, dada2_stats: qiime2.Metadata,
+              nominalq: bool = False, error_in: bool = False,
+              error_out: bool = True):
+
+    # intitalize indexes for html rendering
+    index = os.path.join(TEMPLATES, 'index.html')
+    overview_template = os.path.join(TEMPLATES, 'denoise_stats.html')
+    templates = [index, overview_template]
+    templates.append(os.path.join(TEMPLATES, 'error_plot_stats.html'))
+
+    # convert stats input to dictionary for parsing
+    dada_stats_dict = dict(dada2_stats)
+
+    # initalize data structures for passing to html
+    denoised_reads_data = {}
+    image_paths_arr = []
+    paired_or_not = ''
+
+    # iterate over keys that link to dada2 stats files
+    for keyer in dada_stats_dict.keys():
+
+        # section for dada2 read stats
+        if keyer == 'Denoised_Read_Stats':
+            temp_df = dada_stats_dict[keyer].to_dataframe()
+            for indexer in temp_df.index:
+                row_arr = temp_df.loc[indexer]
+                denoised_reads_data[indexer] \
+                    = {'input': row_arr['input'],
+                        'filtered': row_arr['filtered'],
+                        'per_of_filt': row_arr[
+                            'percentage of input passed filter'],
+                        'denoised': row_arr['denoised'],
+                        'non_chim': row_arr['non-chimeric'],
+                        'per_of_non_chim': row_arr[
+                            'percentage of input non-chimeric']}
+                if 'merged' in temp_df.columns:
+                    paired_or_not = 'paired'
+                    denoised_reads_data[indexer]['merged'] = row_arr['merged']
+                    denoised_reads_data[indexer]['per_input_merged'] = \
+                        row_arr['percentage of input merged']
+                elif 'primer-removed' in temp_df.columns:
+                    paired_or_not = 'ccs'
+                    denoised_reads_data[indexer]['primer_removed'] = \
+                        row_arr['primer-removed']
+                    denoised_reads_data[indexer]['per_prim_removed'] = \
+                        row_arr['percentage of input primer-removed']
+
+        # section for dada2 error plotting
+        elif keyer == 'Error_Plot_Stats':
+            temp_df = dada_stats_dict[keyer].to_dataframe()
+
+            # determines if the reads are paired
+            if len(temp_df.columns.tolist()) > 12:
+                df_fwd_subset = temp_df.iloc[:, :10]
+                df_fwd_subset.columns = \
+                    df_fwd_subset.columns.str.replace('^F_', '', regex=True)
+                df_rev_subset = temp_df.iloc[:, -10:]
+                df_rev_subset.columns = \
+                    df_rev_subset.columns.str.replace('^R_', '', regex=True)
+                image_paths_arr = _plot_errors(df_fwd_subset, image_paths_arr,
+                                               output_dir, "Forward_",
+                                               error_in, error_out, nominalq)
+                image_paths_arr = _plot_errors(df_rev_subset, image_paths_arr,
+                                               output_dir, "Reverse_",
+                                               error_in, error_out, nominalq)
+            else:
+                image_paths_arr = _plot_errors(temp_df, image_paths_arr,
+                                               output_dir, "",
+                                               error_in, error_out, nominalq)
+        else:
+            raise ValueError("Unknown file in metadata folder: (%r)" % keyer)
+    # intializes the context variable for passing to html
+    context = {
+        'tabs': [{'title': 'Denoised-Stats', 'url': 'denoise_stats.html'},
+                 {'title': 'Error-Plot', 'url': 'error_plot_stats.html'}],
+        'denoised_data': denoised_reads_data,
+        'denoised_keys': denoised_reads_data.keys(),
+        'paired_or_not': paired_or_not,
+        'graph_paths': image_paths_arr
+    }
+
+    # renders the template and initalizes the
+    # js sorter for the dada2 read table
+    q2templates.render(templates, output_dir, context=context)
+    js = os.path.join(
+        TEMPLATES, 'js', 'tsorter.min.js')
+    os.mkdir(os.path.join(output_dir, 'js'))
+    shutil.copy(js, os.path.join(output_dir, 'js', 'tsorter.min.js'))

q2_dada2/_dada_stats/assets/denoise_stats.html

@@ -0,0 +1,69 @@
+{% extends "tab-child.html" %}
+
+{% block content %}
+    <table class="table table-striped table-hover" id="denoised_table">
+        <thead>
+        <tr>
+            <th>Sample ID</th>
+            <th data-tsorter="numeric">Input Reads</th>
+            {% if paired_or_not == "ccs" %}
+            <th data-tsorter="numeric">Primer Removed</th>
+            <th data-tsorter="numeric">Percentage of Primer Removed</th>
+            {% endif %}
+            <th data-tsorter="numeric">Filtered Reads</th>
+            <th data-tsorter="numeric">Percentage of Input Passed Filter</th>
+            <th data-tsorter="numeric">Denoised</th>
+            {% if paired_or_not == "paired" %}
+            <th data-tsorter="numeric">Merged</th>
+            <th data-tsorter="numeric">Percentage of Input Merged</th>
+            {% endif %}
+            <th data-tsorter="numeric">Non-Chimeric</th>
+            <th data-tsorter="numeric">Percentage of Input Non-Chimeric</th>
+        </tr>
+        </thead>
+        <tbody>
+        {% for keyer in denoised_keys %}
+        <tr>
+            <td>{{ keyer }}</td>
+            {% if keyer in denoised_data%}
+            <td>{{ denoised_data[keyer].input | int }}</td>
+            {% if paired_or_not == "ccs"  %}
+            <td>{{ denoised_data[keyer].primer_removed| int }}</td>
+            <td>{{ denoised_data[keyer].per_prim_removed | round(2, 'common') }}</td>
+            {% endif %}
+            <td>{{ denoised_data[keyer].filtered | int }}</td>
+            <td>{{ denoised_data[keyer].per_of_filt | round(2, 'common') }}</td>
+            <td>{{ denoised_data[keyer].denoised | int }}</td>
+            {% if paired_or_not == "paired"  %}
+                <td>{{ denoised_data[keyer].merged| int }}</td>
+                <td>{{ denoised_data[keyer].per_input_merged | round(2, 'common') }}</td>
+            {% endif %}
+            <td>{{ denoised_data[keyer].non_chim | int }}</td>
+            <td>{{ denoised_data[keyer].per_of_non_chim | round(2, 'common') }}</td>
+            {% else %}
+            <td>-</td>
+            <td>-</td>
+            {% endif %}
+        </tr>
+        {% endfor %}
+        </tbody>
+    </table>
+
+    <script src="./js/tsorter.min.js" type="text/javascript"></script>
+    <script type="text/javascript">
+      function init() {
+        var sorter = tsorter.create('denoised_table');
+      }
+      window.onload = init;
+    </script>
+    <style media="screen">
+      #seq_table th.descend:after{
+        content: "\25B2";
+      }
+      #seq_table th.ascend:after{
+        content: "\25BC";
+      }
+    </style>
+
+{% endblock %}
+

q2_dada2/_dada_stats/assets/error_plot_stats.html

@@ -0,0 +1,46 @@
+{% extends "tab-child.html" %}
+
+{% block content %}
+
+<style>
+        #imager {
+            display: flex;
+            justify-content: center; 
+            gap: 20px; 
+        }
+        #imager img {
+            max-width: 700px; 
+            height: 700px;     
+            padding: 10px;
+            border: 1px solid black; 
+        }
+</style>
+
+
+{% for index in range(graph_paths|length) %}
+
+<body>
+    <h1 ALIGN=CENTER>
+        {% if graph_paths|length == 1 %}
+
+                DADA2 Error Plot<br>
+
+        {% else %}
+            {% if index == 0 %}
+                    Forward Read DADA2 Error Plot<br>
+            {% else %}
+                    Reverse Read DADA2 Error Plot<br>
+            {% endif %}
+
+        {% endif %}
+    </h1>
+
+    <div id=imager>
+        <div>
+        <img src='{{graph_paths[index]}}' >
+        </div>
+    </div>
+</body>
+{% endfor %}
+
+{% endblock %}

q2_dada2/_dada_stats/assets/index.html

@@ -0,0 +1 @@
+{% extends "tab-parent.html" %}