{"action":"created","comment":{"url":"https://api.github.com/repos/NationalGenomicsInfrastructure/ngi_visualizations/pulls/comments/88638904","pull_request_review_id":9196863,"id":88638904,"diff_hunk":"@@ -26,57 +29,90 @@ def make_fpkm_scatter_plots (input_files, summary=False, output_fn='gene_counts'\n     \"\"\"\n     Main function. Takes input files and makes a plot.\n     \"\"\"\n-    \n-    # Get proper paths for input files\n-    input_1 = os.path.realpath(input_files[0])\n-    input_2 = os.path.realpath(input_files[1])\n-    \n-    # First off, assume that we have two FPKM files from cufflinks\n-    if summary is False:\n-       \n-        # Parse the input files\n-        sample_1 = load_fpkm_counts(input_1)\n-        sample_2 = load_fpkm_counts(input_2)\n-        \n-        # What are the sample names?\n-        sample_1_name = os.path.splitext(os.path.basename(input_1))[0]\n-        sample_2_name = os.path.splitext(os.path.basename(input_2))[0]\n+    R_dict={}\n+    #iterate over all uniqe pairs of input files\n+    for f,y in itertools.combinations(input_files,2):\n+        # Get proper paths for input files\n+        input_1 = os.path.realpath(f)\n+        input_2 = os.path.realpath(y)\n         \n-        # File name\n-        if output_fn is None:\n-            output_fn = \"{}-{}\".format(sample_1_name, sample_2_name)\n+        # First off, assume that we have two FPKM files from cufflinks\n+        if summary is False:\n+           \n+            # Parse the input files\n+            sample_1 = load_fpkm_counts(input_1)\n+            sample_2 = load_fpkm_counts(input_2)\n+            \n+            # What are the sample names?\n+            sample_1_name = os.path.splitext(os.path.basename(input_1))[0]\n+            sample_2_name = os.path.splitext(os.path.basename(input_2))[0]\n+            #print(sample_1_name)\n+            #print(sample_2_name)\n+            # File name\n+            if output_fn is None:\n+                output_fn=False\n+            # Make the plot\n+            plot_filenames = plot_fpkm_scatter(sample_1, sample_2, sample_1_name, sample_2_name, output_fn=output_fn, linear=linear)\n+            #Extract the R-value\n+            #Get the key from the sample names \n+            fn_key = \"{}-{}\".format(sample_1_name, sample_2_name) \n+            R_dict[fn_key]= plot_filenames[fn_key]\n+        # We have a summary file\n+        else:\n+            # Parse the input files\n+            # returns counts[sample_name][gene_id] = fpkm_count\n+            condition_1 = load_summary_fpkm_counts(input_1)\n+            condition_2 = load_summary_fpkm_counts(input_2)\n+            \n+            # Condition basenames\n+            cond_1_basename = os.path.splitext(os.path.basename(input_1))[0]\n+            cond_2_basename = os.path.splitext(os.path.basename(input_2))[0]\n+            \n+            # Find project names from sample ID (P1234_*)\n+            pname_re = re.compile('^P\\d+_')","path":"ngi_visualizations/fpkm_scatter/fpkm_scatter.py","position":83,"original_position":83,"commit_id":"f0571be7579c0957a745a024a414199dda5aac59","original_commit_id":"f0571be7579c0957a745a024a414199dda5aac59","user":{"login":"ewels","id":465550,"avatar_url":"https://avatars.githubusercontent.com/u/465550?v=3","gravatar_id":"","url":"https://api.github.com/users/ewels","html_url":"https://github.com/ewels","followers_url":"https://api.github.com/users/ewels/followers","following_url":"https://api.github.com/users/ewels/following{/other_user}","gists_url":"https://api.github.com/users/ewels/gists{/gist_id}","starred_url":"https://api.github.com/users/ewels/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ewels/subscriptions","organizations_url":"https://api.github.com/users/ewels/orgs","repos_url":"https://api.github.com/users/ewels/repos","events_url":"https://api.github.com/users/ewels/events{/privacy}","received_events_url":"https://api.github.com/users/ewels/received_events","type":"User","site_admin":false},"body":"If you want to get the id without the underscore, use `'^(P\\d+)_'`, then `group(1)`. I also usually specify how many numbers I expect - `'^(P\\d{3,5})_'`","created_at":"2016-11-18T11:09:34Z","updated_at":"2016-11-18T11:09:34Z","html_url":"https://github.com/NationalGenomicsInfrastructure/ngi_visualizations/pull/29#discussion_r88638904","pull_request_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/ngi_visualizations/pulls/29","_links":{"self":{"href":"https://api.github.com/repos/NationalGenomicsInfrastructure/ngi_visualizations/pulls/comments/88638904"},"html":{"href":"https://github.com/NationalGenomicsInfrastructure/ngi_visualizations/pull/29#discussion_r88638904"},"pull_request":{"href":"https://api.github.com/repos/NationalGenomicsInfrastructure/ngi_visualizations/pulls/29"}}},"pull_request":{"url":"https://api.github.com/repos/NationalGenomicsInfrastructure/ngi_visualizations/pulls/29","id":94332780,"html_url":"https://github.com/NationalGenomicsInfrastructure/ngi_visualizations/pull/29","diff_url":"https://github.com/NationalGenomicsInfrastructure/ngi_visualizations/pull/29.diff","patch_url":"https://github.com/NationalGenomicsInfrastructure/ngi_visualizations/pull/29.patch","issue_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/ngi_visualizations/issues/29","number":29,"state":"open","locked":false,"title":"Update to fmpk_scatterplot.py","user":{"login":"Hammarn","id":16774076,"avatar_url":"https://avatars.githubusercontent.com/u/16774076?v=3","gravatar_id":"","url":"https://api.github.com/users/Hammarn","html_url":"https://github.com/Hammarn","followers_url":"https://api.github.com/users/Hammarn/followers","following_url":"https://api.github.com/users/Hammarn/following{/other_user}","gists_url":"https://api.github.com/users/Hammarn/gists{/gist_id}","starred_url":"https://api.github.com/users/Hammarn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Hammarn/subscriptions","organizations_url":"https://api.github.com/users/Hammarn/orgs","repos_url":"https://api.github.com/users/Hammarn/repos","events_url":"https://api.github.com/users/Hammarn/events{/privacy}","received_events_url":"https://api.github.com/users/Hammarn/received_events","type":"User","site_admin":false},"body":"Two main things:\r\n\r\n1. The script can now take a list of FPKM files for input and do pairwise comparisons of them all. (only one pair previously)\r\n\r\n2. R2 values for these multiple samples are now saved into a data matrix in a `.csv` file and to a heat map `png`file.","created_at":"2016-11-18T10:00:21Z","updated_at":"2016-11-18T11:29:28Z","closed_at":null,"merged_at":null,"merge_commit_sha":"9fe60c06a1b417a9ae3b87b6970d26fb61dcb1e6","assignee":{"login":"ewels","id":465550,"avatar_url":"https://avatars.githubusercontent.com/u/465550?v=3","gravatar_id":"","url":"https://api.github.com/users/ewels","html_url":"https://github.com/ewels","followers_url":"https://api.github.com/users/ewels/followers","following_url":"https://api.github.com/users/ewels/following{/other_user}","gists_url":"https://api.github.com/users/ewels/gists{/gist_id}","starred_url":"https://api.github.com/users/ewels/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ewels/subscriptions","organizations_url":"https://api.github.com/users/ewels/orgs","repos_url":"https://api.github.com/users/ewels/repos","events_url":"https://api.github.com/users/ewels/events{/privacy}","received_events_url":"https://api.github.com/users/ewels/received_events","type":"User","site_admin":false},"assignees":[{"login":"ewels","id":465550,"avatar_url":"https://avatars.githubusercontent.com/u/465550?v=3","gravatar_id":"","url":"https://api.github.com/users/ewels","html_url":"https://github.com/ewels","followers_url":"https://api.github.com/users/ewels/followers","following_url":"https://api.github.com/users/ewels/following{/other_user}","gists_url":"https://api.github.com/users/ewels/gists{/gist_id}","starred_url":"https://api.github.com/users/ewels/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ewels/subscriptions","organizations_url":"https://api.github.com/users/ewels/orgs","repos_url":"https://api.github.com/users/ewels/repos","events_url":"https://api.github.com/users/ewels/events{/privacy}","received_events_url":"https://api.github.com/users/ewels/received_events","type":"User","site_admin":false}],"milestone":null,"commits_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/ngi_visualizations/pulls/29/commits","review_comments_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/ngi_visualizations/pulls/29/comments","review_comment_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/ngi_visualizations/pulls/comments{/number}","comments_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/ngi_visualizations/issues/29/comments","statuses_url":"https://api.github.com/repos/NationalGenomicsInfrastructure/ngi_visualizations/statuses/f0571be7579c0957a745a024a414199dda5aac59","head":{"label":"Hammarn:master","ref":"master","sha":"f0571be7579c0957a745a024a414199dda5aac59","user":{"login":"Hammarn","id":16774076,"avatar_url":"https://avatars.githubusercontent.com/u/16774076?v=3","gravatar_id":"","url":"https://api.github.com/users/Hammarn","html_url":"https://github.com/Hammarn","followers_url":"https://api.github.com/users/Hammarn/followers","following_url":"https://api.github.com/users/Hammarn/following{/other_user}","gists_url":"https://api.github.com/users/Hammarn/gists{/gist_id}","starred_url":"https://api.github.com/users/Hammarn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Hammarn/subscriptions","organizations_url":"https://api.github.com/users/Hammarn/orgs","repos_url":"https://api.github.com/users/Hammarn/repos","events_url":"https://api.github.com/users/Hammarn/events{/privacy}","received_events_url":"https://api.github.com/users/Hammarn/received_events","type":"User","site_admin":false},"repo":{"id":73461235,"name":"ngi_visualizations","full_name":"Hammarn/ngi_visualizations","owner":{"login":"Hammarn","id":16774076,"avatar_url":"https://avatars.githubusercontent.com/u/16774076?v=3","gravatar_id":"","url":"https://api.github.com/users/Hammarn","html_url":"https://github.com/Hammarn","followers_url":"https://api.github.com/users/Hammarn/followers","following_url":"https://api.github.com/users/Hammarn/following{/other_user}","gists_url":"https://api.github.com/users/Hammarn/gists{/gist_id}","starred_url":"https://api.github.com/users/Hammarn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Hammarn/subscriptions","organizations_url":"https://api.github.com/users/Hammarn/orgs","repos_url":"https://api.github.com/users/Hammarn/repos","events_url":"https://api.github.com/users/Hammarn/events{/privacy}","received_events_url":"https://api.github.com/users/Hammarn/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/Hammarn/ngi_visualizations","description":"Next-Gen 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