Mercurial > repos > bgruening > sklearn_regression_metrics

changeset 37:6db5c1dfb076 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
author bgruening
date Fri, 22 Sep 2023 16:49:59 +0000
parents f5dcb87fd14e
children dc17e2878dc1
files ml_visualization_ex.py pdb70_cs219.ffdata
diffstat 2 files changed, 79 insertions(+), 189 deletions(-) [+]
line wrap: on
line diff
--- a/ml_visualization_ex.py	Wed Aug 09 15:11:03 2023 +0000
+++ b/ml_visualization_ex.py	Fri Sep 22 16:49:59 2023 +0000
@@ -15,6 +15,7 @@
 from sklearn.metrics import (
     auc,
     average_precision_score,
+    confusion_matrix,
     precision_recall_curve,
     roc_curve,
 )
@@ -258,6 +259,30 @@
     os.rename(os.path.join(folder, "output.svg"), os.path.join(folder, "output"))
 
 
+def get_dataframe(file_path, plot_selection, header_name, column_name):
+    header = "infer" if plot_selection[header_name] else None
+    column_option = plot_selection[column_name]["selected_column_selector_option"]
+    if column_option in [
+        "by_index_number",
+        "all_but_by_index_number",
+        "by_header_name",
+        "all_but_by_header_name",
+    ]:
+        col = plot_selection[column_name]["col1"]
+    else:
+        col = None
+    _, input_df = read_columns(
+        file_path,
+        c=col,
+        c_option=column_option,
+        return_df=True,
+        sep="\t",
+        header=header,
+        parse_dates=True,
+    )
+    return input_df
+
+
 def main(
     inputs,
     infile_estimator=None,
@@ -271,6 +296,10 @@
     targets=None,
     fasta_path=None,
     model_config=None,
+    true_labels=None,
+    predicted_labels=None,
+    plot_color=None,
+    title=None,
 ):
     """
     Parameter
@@ -311,6 +340,18 @@
 
     model_config : str, default is None
         File path to dataset containing JSON config for neural networks
+
+    true_labels : str, default is None
+        File path to dataset containing true labels
+
+    predicted_labels : str, default is None
+        File path to dataset containing true predicted labels
+
+    plot_color : str, default is None
+        Color of the confusion matrix heatmap
+
+    title : str, default is None
+        Title of the confusion matrix heatmap
     """
     warnings.simplefilter("ignore")
 
@@ -534,6 +575,36 @@
 
         return 0
 
+    elif plot_type == "classification_confusion_matrix":
+        plot_selection = params["plotting_selection"]
+        input_true = get_dataframe(
+            true_labels, plot_selection, "header_true", "column_selector_options_true"
+        )
+        header_predicted = "infer" if plot_selection["header_predicted"] else None
+        input_predicted = pd.read_csv(
+            predicted_labels, sep="\t", parse_dates=True, header=header_predicted
+        )
+        true_classes = input_true.iloc[:, -1].copy()
+        predicted_classes = input_predicted.iloc[:, -1].copy()
+        axis_labels = list(set(true_classes))
+        c_matrix = confusion_matrix(true_classes, predicted_classes)
+        fig, ax = plt.subplots(figsize=(7, 7))
+        im = plt.imshow(c_matrix, cmap=plot_color)
+        for i in range(len(c_matrix)):
+            for j in range(len(c_matrix)):
+                ax.text(j, i, c_matrix[i, j], ha="center", va="center", color="k")
+        ax.set_ylabel("True class labels")
+        ax.set_xlabel("Predicted class labels")
+        ax.set_title(title)
+        ax.set_xticks(axis_labels)
+        ax.set_yticks(axis_labels)
+        fig.colorbar(im, ax=ax)
+        fig.tight_layout()
+        plt.savefig("output.png", dpi=125)
+        os.rename("output.png", "output")
+
+        return 0
+
     # save pdf file to disk
     # fig.write_image("image.pdf", format='pdf')
     # fig.write_image("image.pdf", format='pdf', width=340*2, height=226*2)
@@ -553,6 +624,10 @@
     aparser.add_argument("-t", "--targets", dest="targets")
     aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
     aparser.add_argument("-c", "--model_config", dest="model_config")
+    aparser.add_argument("-tl", "--true_labels", dest="true_labels")
+    aparser.add_argument("-pl", "--predicted_labels", dest="predicted_labels")
+    aparser.add_argument("-pc", "--plot_color", dest="plot_color")
+    aparser.add_argument("-pt", "--title", dest="title")
     args = aparser.parse_args()
 
     main(
@@ -568,4 +643,8 @@
         targets=args.targets,
         fasta_path=args.fasta_path,
         model_config=args.model_config,
+        true_labels=args.true_labels,
+        predicted_labels=args.predicted_labels,
+        plot_color=args.plot_color,
+        title=args.title,
     )
--- a/pdb70_cs219.ffdata	Wed Aug 09 15:11:03 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,189 +0,0 @@
-
-
-
-
-<!DOCTYPE HTML>
-<html>
-    <!--base.mako-->
-    
-
-
-    <head>
-        <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-        <meta name = "viewport" content = "maximum-scale=1.0">
-        <meta http-equiv="X-UA-Compatible" content="IE=Edge,chrome=1">
-
-        <title>
-            Galaxy
-            | Europe
-            | 
-        </title>
-
-        <link rel="index" href="/"/>
-
-        
-        
-    <link href="/static/style/bootstrap-tour.css?v=1618364054" media="screen" rel="stylesheet" type="text/css" />
-    <link href="/static/dist/base.css?v=1618364054" media="screen" rel="stylesheet" type="text/css" />
-
-        
-    <script src="/static/dist/libs.chunk.js?v=1618364054" type="text/javascript"></script>
-<script src="/static/dist/base.chunk.js?v=1618364054" type="text/javascript"></script>
-<script src="/static/dist/generic.bundled.js?v=1618364054" type="text/javascript"></script>
-
-        
-    <!-- message.mako javascript_app() -->
-    
-
-    
-    <script type="text/javascript">
-        // galaxy_client_app.mako, load
-
-        var bootstrapped;
-        try {
-            bootstrapped = 
-{}
-;
-        } catch(err) {
-            console.warn("Unable to parse bootstrapped variable", err);
-            bootstrapped = {};
-        }
-
-        var options = {
-            root: '/',
-            config: 
-    
-{
-"display_galaxy_brand": true,
-"chunk_upload_size": 104857600,
-"use_remote_user": null,
-"enable_oidc": true,
-"mailing_join_addr": null,
-"select_type_workflow_threshold": -1,
-"myexperiment_target_url": "www.myexperiment.org:80",
-"tool_recommendation_model_path": "https://github.com/galaxyproject/galaxy-test-data/raw/master/tool_recommendation_model.hdf5",
-"simplified_workflow_run_ui_target_history": "current",
-"interactivetools_enable": true,
-"is_admin_user": false,
-"show_welcome_with_login": true,
-"welcome_url": "/static/welcome.html",
-"allow_user_impersonation": true,
-"overwrite_model_recommendations": false,
-"topk_recommendations": 10,
-"user_library_import_dir_available": false,
-"ga_code": null,
-"enable_beta_markdown_export": true,
-"visualizations_visible": true,
-"enable_tool_recommendations": true,
-"enable_unique_workflow_defaults": false,
-"registration_warning_message": "Please register only one account. The usegalaxy.eu service is provided free of charge and has limited computational and data storage resources. <strong>Registration and usage of multiple accounts is tracked and such accounts are subject to termination and data deletion.<\/strong>",
-"logo_src": "/static/favicon.png",
-"enable_quotas": true,
-"server_mail_configured": true,
-"citation_url": "https://galaxyproject.org/citing-galaxy",
-"allow_user_dataset_purge": true,
-"ftp_upload_site": "ftp://ftp.usegalaxy.eu",
-"terms_url": "https://usegalaxy.eu/terms",
-"upload_from_form_button": "always-on",
-"wiki_url": "https://galaxyproject.org/",
-"logo_src_secondary": null,
-"aws_estimate": true,
-"single_user": false,
-"datatypes_disable_auto": false,
-"brand": "Europe",
-"mailing_lists": "https://galaxyproject.org/mailing-lists/",
-"python": [
-3,
-6
-],
-"release_doc_base_url": "https://docs.galaxyproject.org/en/release_",
-"enable_openid": false,
-"cookie_domain": null,
-"message_box_content": "You are using the new UseGalaxy.eu backend server, let us know if you encounter any issues!",
-"admin_tool_recommendations_path": "/opt/galaxy/config/tool_recommendations_overwrite.yml",
-"search_url": "https://galaxyproject.org/search/",
-"remote_user_logout_href": null,
-"default_locale": "auto",
-"screencasts_url": "https://vimeo.com/galaxyproject",
-"quota_url": "https://galaxyproject.org/support/account-quotas/",
-"version_major": "21.01",
-"simplified_workflow_run_ui": "prefer",
-"allow_user_creation": true,
-"lims_doc_url": "https://usegalaxy.org/u/rkchak/p/sts",
-"message_box_visible": false,
-"has_user_tool_filters": true,
-"message_box_class": "info",
-"require_login": false,
-"logo_url": "/",
-"support_url": "https://galaxyproject.org/support/",
-"simplified_workflow_run_ui_job_cache": "off",
-"server_startttime": 1618364054,
-"oidc": {
-"elixir": {
-"icon": "https://elixir-europe.org/sites/default/files/images/login-button-orange.png"
-}
-},
-"version_minor": "",
-"helpsite_url": "https://help.galaxyproject.org/c/usegalaxy-eu-support",
-"file_sources_configured": true,
-"inactivity_box_content": "Your account has not been activated yet.  Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address.",
-"nginx_upload_path": "/_upload"
-}
-,
-            user: 
-    
-{
-"total_disk_usage": 0,
-"nice_total_disk_usage": "0 bytes",
-"quota_percent": null
-}
-,
-            session_csrf_token: 'c3ae71f65be7de55dd5bd5f97f316000'
-        };
-
-        config.set({
-            options: options,
-            bootstrapped: bootstrapped
-        });
-
-
-    </script>
-
-    
-
-
-
-
-    
-
-    
-    <script type="text/javascript">
-        config.addInitialization(function() {
-            if (parent.handle_minwidth_hint) {
-                parent.handle_minwidth_hint(-1);
-            }
-        });
-    </script>
-
-    </head>
-    <body class="inbound">
-        
-    
-    
-    <div class="message mt-2 alert alert-danger">You are not allowed to access this dataset</div>
-
-
-    </body>
-</html>
-
-
-
-
-
-
-
-
-
-
-
-