{"action":"created","comment":{"url":"https://api.github.com/repos/thehyve/heim-SmartR/pulls/comments/47792183","id":47792183,"diff_hunk":"@@ -10,36 +14,37 @@ main <- function(max_rows = 100, sorting = \"nodes\") {\n                                        # prevent problems with CSS\n                                        # selectors on the frontend.\n   write.table(\n-      df,\n-      \"heatmap_orig_values.tsv\",\n-      sep = \"\\t\",\n-      na = \"\",\n-      row.names = FALSE,\n-      col.names = TRUE\n-    )\n-  df          <- addStats(df, sorting)\n-  df          <- df[1:min(max_rows,nrow(df)),]  #  apply max_rows\n+    df,\n+    \"heatmap_orig_values.tsv\",\n+    sep = \"\\t\",\n+    na = \"\",\n+    row.names = FALSE,\n+    col.names = TRUE\n+  )\n+  df          <- addStats(df, sorting, ranking, max_rows)\n+  df          <- df[1:min(max_rows, nrow(df)), ]  #  apply max_rows\n   fields      <- buildFields(df)\n   extraFields <- buildExtraFields(fields)\n-  probes      <- df[,1]\n-  geneSymbols <- df[,2]\n+  probes      <- df[, 1]\n+  geneSymbols <- df[, 2]\n   #unique(fields[\"GENESYMBOL\"])[,1] #[,1] in order to get a vector,\n   # otherwise we get a dataframe\n   patientIDs  <- unique(fields[\"PATIENTID\"])[,1]\n-  \n+\n   significanceValues <- unique(fields[\"SIGNIFICANCE\"])[,1]\n   features <- unique(extraFields[\"FEATURE\"])[,1]\n   jsn <- list(\n-    \"fields\" = fields, \"geneSymbols\" = geneSymbols,\n-    \"patientIDs\" = patientIDs,\n-    \"probes\" = probes,\n+    \"fields\"             = fields,\n+    \"geneSymbols\"        = geneSymbols,\n+    \"patientIDs\"         = patientIDs,\n+    \"probes\"             = probes,\n     \"significanceValues\" = significanceValues,\n-    \"features\" = features,\n-    \"extraFields\" = extraFields\n+    \"features\"           = features,\n+    \"extraFields\"        = extraFields\n   )\n   writeRunParams(max_rows, sorting)\n   measurements <- cleanUp(df)  # temporary stats like SD and MEAN need\n-                     # to be removed for clustering to work\n+                               # to be removed for clustering to work\n   measurements <- measurements[,3:ncol(measurements)]","path":"web-app/HeimScripts/heatmap/run.R","position":65,"original_position":65,"commit_id":"8bd3afab46cdf7653c2aa89ac3a35e2063e1bb73","original_commit_id":"1a65c4c7121f5d63859eb5b08d12185503633f7c","user":{"login":"RianneJ","id":6952296,"avatar_url":"https://avatars.githubusercontent.com/u/6952296?v=3","gravatar_id":"","url":"https://api.github.com/users/RianneJ","html_url":"https://github.com/RianneJ","followers_url":"https://api.github.com/users/RianneJ/followers","following_url":"https://api.github.com/users/RianneJ/following{/other_user}","gists_url":"https://api.github.com/users/RianneJ/gists{/gist_id}","starred_url":"https://api.github.com/users/RianneJ/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/RianneJ/subscriptions","organizations_url":"https://api.github.com/users/RianneJ/orgs","repos_url":"https://api.github.com/users/RianneJ/repos","events_url":"https://api.github.com/users/RianneJ/events{/privacy}","received_events_url":"https://api.github.com/users/RianneJ/received_events","type":"User","site_admin":false},"body":"nitpicking at its finest: getMeasurements()?","created_at":"2015-12-16T15:48:38Z","updated_at":"2015-12-16T15:48:38Z","html_url":"https://github.com/thehyve/heim-SmartR/pull/80#discussion_r47792183","pull_request_url":"https://api.github.com/repos/thehyve/heim-SmartR/pulls/80","_links":{"self":{"href":"https://api.github.com/repos/thehyve/heim-SmartR/pulls/comments/47792183"},"html":{"href":"https://github.com/thehyve/heim-SmartR/pull/80#discussion_r47792183"},"pull_request":{"href":"https://api.github.com/repos/thehyve/heim-SmartR/pulls/80"}}},"pull_request":{"url":"https://api.github.com/repos/thehyve/heim-SmartR/pulls/80","id":53833296,"html_url":"https://github.com/thehyve/heim-SmartR/pull/80","diff_url":"https://github.com/thehyve/heim-SmartR/pull/80.diff","patch_url":"https://github.com/thehyve/heim-SmartR/pull/80.patch","issue_url":"https://api.github.com/repos/thehyve/heim-SmartR/issues/80","number":80,"state":"open","locked":false,"title":"Marker selection r","user":{"login":"PiotrZakrzewski","id":1050269,"avatar_url":"https://avatars.githubusercontent.com/u/1050269?v=3","gravatar_id":"","url":"https://api.github.com/users/PiotrZakrzewski","html_url":"https://github.com/PiotrZakrzewski","followers_url":"https://api.github.com/users/PiotrZakrzewski/followers","following_url":"https://api.github.com/users/PiotrZakrzewski/following{/other_user}","gists_url":"https://api.github.com/users/PiotrZakrzewski/gists{/gist_id}","starred_url":"https://api.github.com/users/PiotrZakrzewski/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PiotrZakrzewski/subscriptions","organizations_url":"https://api.github.com/users/PiotrZakrzewski/orgs","repos_url":"https://api.github.com/users/PiotrZakrzewski/repos","events_url":"https://api.github.com/users/PiotrZakrzewski/events{/privacy}","received_events_url":"https://api.github.com/users/PiotrZakrzewski/received_events","type":"User","site_admin":false},"body":"","created_at":"2015-12-16T12:11:10Z","updated_at":"2015-12-16T15:48:38Z","closed_at":null,"merged_at":null,"merge_commit_sha":"54ec6ce43661739fdab8676b30462c5d973a2a93","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/thehyve/heim-SmartR/pulls/80/commits","review_comments_url":"https://api.github.com/repos/thehyve/heim-SmartR/pulls/80/comments","review_comment_url":"https://api.github.com/repos/thehyve/heim-SmartR/pulls/comments{/number}","comments_url":"https://api.github.com/repos/thehyve/heim-SmartR/issues/80/comments","statuses_url":"https://api.github.com/repos/thehyve/heim-SmartR/statuses/8bd3afab46cdf7653c2aa89ac3a35e2063e1bb73","head":{"label":"thehyve:marker-selection-r","ref":"marker-selection-r","sha":"8bd3afab46cdf7653c2aa89ac3a35e2063e1bb73","user":{"login":"thehyve","id":1502440,"avatar_url":"https://avatars.githubusercontent.com/u/1502440?v=3","gravatar_id":"","url":"https://api.github.com/users/thehyve","html_url":"https://github.com/thehyve","followers_url":"https://api.github.com/users/thehyve/followers","following_url":"https://api.github.com/users/thehyve/following{/other_user}","gists_url":"https://api.github.com/users/thehyve/gists{/gist_id}","starred_url":"https://api.github.com/users/thehyve/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thehyve/subscriptions","organizations_url":"https://api.github.com/users/thehyve/orgs","repos_url":"https://api.github.com/users/thehyve/repos","events_url":"https://api.github.com/users/thehyve/events{/privacy}","received_events_url":"https://api.github.com/users/thehyve/received_events","type":"Organization","site_admin":false},"repo":{"id":43434009,"name":"heim-SmartR","full_name":"thehyve/heim-SmartR","owner":{"login":"thehyve","id":1502440,"avatar_url":"https://avatars.githubusercontent.com/u/1502440?v=3","gravatar_id":"","url":"https://api.github.com/users/thehyve","html_url":"https://github.com/thehyve","followers_url":"https://api.github.com/users/thehyve/followers","following_url":"https://api.github.com/users/thehyve/following{/other_user}","gists_url":"https://api.github.com/users/thehyve/gists{/gist_id}","starred_url":"https://api.github.com/users/thehyve/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thehyve/subscriptions","organizations_url":"https://api.github.com/users/thehyve/orgs","repos_url":"https://api.github.com/users/thehyve/repos","events_url":"https://api.github.com/users/thehyve/events{/privacy}","received_events_url":"https://api.github.com/users/thehyve/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/thehyve/heim-SmartR","description":"heim","fork":false,"url":"https://api.github.com/repos/thehyve/heim-SmartR","forks_url":"https://api.github.com/repos/thehyve/heim-SmartR/forks","keys_url":"https://api.github.com/repos/thehyve/heim-SmartR/keys{/key_id}","collaborators_url":"https://api.github.com/repos/thehyve/heim-SmartR/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/thehyve/heim-SmartR/teams","hooks_url":"https://api.github.com/repos/thehyve/heim-SmartR/hooks","issue_events_url":"https://api.github.com/repos/thehyve/heim-SmartR/issues/events{/number}","events_url":"https://api.github.com/repos/thehyve/heim-SmartR/events","assignees_url":"https://api.github.com/repos/thehyve/heim-SmartR/assignees{/user}","branches_url":"https://api.github.com/repos/thehyve/heim-SmartR/branches{/branch}","tags_url":"https://api.github.com/repos/thehyve/heim-SmartR/tags","blobs_url":"https://api.github.com/repos/thehyve/heim-SmartR/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/thehyve/heim-SmartR/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/thehyve/heim-SmartR/git/refs{/sha}","trees_url":"https://api.github.com/repos/thehyve/heim-SmartR/git/trees{/sha}","statuses_url":"https://api.github.com/repos/thehyve/heim-SmartR/statuses/{sha}","languages_url":"https://api.github.com/repos/thehyve/heim-SmartR/languages","stargazers_url":"https://api.github.com/repos/thehyve/heim-SmartR/stargazers","contributors_url":"https://api.github.com/repos/thehyve/heim-SmartR/contributors","subscribers_url":"https://api.github.com/repos/thehyve/heim-SmartR/subscribers","subscription_url":"https://api.github.com/repos/thehyve/heim-SmartR/subscription","commits_url":"https://api.github.com/repos/thehyve/heim-SmartR/commits{/sha}","git_commits_url":"https://api.github.com/repos/thehyve/heim-SmartR/git/commits{/sha}","comments_url":"https://api.github.com/repos/thehyve/heim-SmartR/comments{/number}","issue_comment_url":"https://api.github.com/repos/thehyve/heim-SmartR/issues/comments{/number}","contents_url":"https://api.github.com/repos/thehyve/heim-SmartR/contents/{+path}","compare_url":"https://api.github.com/repos/thehyve/heim-SmartR/compare/{base}...{head}","merges_url":"https://api.github.com/repos/thehyve/heim-SmartR/merges","archive_url":"https://api.github.com/repos/thehyve/heim-SmartR/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/thehyve/heim-SmartR/downloads","issues_url":"https://api.github.com/repos/thehyve/heim-SmartR/issues{/number}","pulls_url":"https://api.github.com/repos/thehyve/heim-SmartR/pulls{/number}","milestones_url":"https://api.github.com/repos/thehyve/heim-SmartR/milestones{/number}","notifications_url":"https://api.github.com/repos/thehyve/heim-SmartR/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/thehyve/heim-SmartR/labels{/name}","releases_url":"https://api.github.com/repos/thehyve/heim-SmartR/releases{/id}","created_at":"2015-09-30T13:19:44Z","updated_at":"2015-12-03T13:40:14Z","pushed_at":"2015-12-16T15:36:28Z","git_url":"git://github.com/thehyve/heim-SmartR.git","ssh_url":"git@github.com:thehyve/heim-SmartR.git","clone_url":"https://github.com/thehyve/heim-SmartR.git","svn_url":"https://github.com/thehyve/heim-SmartR","homepage":"","size":2274,"stargazers_count":1,"watchers_count":1,"language":"JavaScript","has_issues":false,"has_downloads":true,"has_wiki":false,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":1,"forks":0,"open_issues":1,"watchers":1,"default_branch":"dev"}},"base":{"label":"thehyve:dev","ref":"dev","sha":"6f8487c7db5bfe2dca2baa3fc32b04ab551e824e","user":{"login":"thehyve","id":1502440,"avatar_url":"https://avatars.githubusercontent.com/u/1502440?v=3","gravatar_id":"","url":"https://api.github.com/users/thehyve","html_url":"https://github.com/thehyve","followers_url":"https://api.github.com/users/thehyve/followers","following_url":"https://api.github.com/users/thehyve/following{/other_user}","gists_url":"https://api.github.com/users/thehyve/gists{/gist_id}","starred_url":"https://api.github.com/users/thehyve/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thehyve/subscriptions","organizations_url":"https://api.github.com/users/thehyve/orgs","repos_url":"https://api.github.com/users/thehyve/repos","events_url":"https://api.github.com/users/thehyve/events{/privacy}","received_events_url":"https://api.github.com/users/thehyve/received_events","type":"Organization","site_admin":false},"repo":{"id":43434009,"name":"heim-SmartR","full_name":"thehyve/heim-SmartR","owner":{"login":"thehyve","id":1502440,"avatar_url":"https://avatars.githubusercontent.com/u/1502440?v=3","gravatar_id":"","url":"https://api.github.com/users/thehyve","html_url":"https://github.com/thehyve","followers_url":"https://api.github.com/users/thehyve/followers","following_url":"https://api.github.com/users/thehyve/following{/other_user}","gists_url":"https://api.github.com/users/thehyve/gists{/gist_id}","starred_url":"https://api.github.com/users/thehyve/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thehyve/subscriptions","organizations_url":"https://api.github.com/users/thehyve/orgs","repos_url":"https://api.github.com/users/thehyve/repos","events_url":"https://api.github.com/users/thehyve/events{/privacy}","received_events_url":"https://api.github.com/users/thehyve/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/thehyve/heim-SmartR","description":"heim","fork":false,"url":"https://api.github.com/repos/thehyve/heim-SmartR","forks_url":"https://api.github.com/repos/thehyve/heim-SmartR/forks","keys_url":"https://api.github.com/repos/thehyve/heim-SmartR/keys{/key_id}","collaborators_url":"https://api.github.com/repos/thehyve/heim-SmartR/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/thehyve/heim-SmartR/teams","hooks_url":"https://api.github.com/repos/thehyve/heim-SmartR/hooks","issue_events_url":"https://api.github.com/repos/thehyve/heim-SmartR/issues/events{/number}","events_url":"https://api.github.com/repos/thehyve/heim-SmartR/events","assignees_url":"https://api.github.com/repos/thehyve/heim-SmartR/assignees{/user}","branches_url":"https://api.github.com/repos/thehyve/heim-SmartR/branches{/branch}","tags_url":"https://api.github.com/repos/thehyve/heim-SmartR/tags","blobs_url":"https://api.github.com/repos/thehyve/heim-SmartR/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/thehyve/heim-SmartR/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/thehyve/heim-SmartR/git/refs{/sha}","trees_url":"https://api.github.com/repos/thehyve/heim-SmartR/git/trees{/sha}","statuses_url":"https://api.github.com/repos/thehyve/heim-SmartR/statuses/{sha}","languages_url":"https://api.github.com/repos/thehyve/heim-SmartR/languages","stargazers_url":"https://api.github.com/repos/thehyve/heim-SmartR/stargazers","contributors_url":"https://api.github.com/repos/thehyve/heim-SmartR/contributors","subscribers_url":"https://api.github.com/repos/thehyve/heim-SmartR/subscribers","subscription_url":"https://api.github.com/repos/thehyve/heim-SmartR/subscription","commits_url":"https://api.github.com/repos/thehyve/heim-SmartR/commits{/sha}","git_commits_url":"https://api.github.com/repos/thehyve/heim-SmartR/git/commits{/sha}","comments_url":"https://api.github.com/repos/thehyve/heim-SmartR/comments{/number}","issue_comment_url":"https://api.github.com/repos/thehyve/heim-SmartR/issues/comments{/number}","contents_url":"https://api.github.com/repos/thehyve/heim-SmartR/contents/{+path}","compare_url":"https://api.github.com/repos/thehyve/heim-SmartR/compare/{base}...{head}","merges_url":"https://api.github.com/repos/thehyve/heim-SmartR/merges","archive_url":"https://api.github.com/repos/thehyve/heim-SmartR/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/thehyve/heim-SmartR/downloads","issues_url":"https://api.github.com/repos/thehyve/heim-SmartR/issues{/number}","pulls_url":"https://api.github.com/repos/thehyve/heim-SmartR/pulls{/number}","milestones_url":"https://api.github.com/repos/thehyve/heim-SmartR/milestones{/number}","notifications_url":"https://api.github.com/repos/thehyve/heim-SmartR/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/thehyve/heim-SmartR/labels{/name}","releases_url":"https://api.github.com/repos/thehyve/heim-SmartR/releases{/id}","created_at":"2015-09-30T13:19:44Z","updated_at":"2015-12-03T13:40:14Z","pushed_at":"2015-12-16T15:36:28Z","git_url":"git://github.com/thehyve/heim-SmartR.git","ssh_url":"git@github.com:thehyve/heim-SmartR.git","clone_url":"https://github.com/thehyve/heim-SmartR.git","svn_url":"https://github.com/thehyve/heim-SmartR","homepage":"","size":2274,"stargazers_count":1,"watchers_count":1,"language":"JavaScript","has_issues":false,"has_downloads":true,"has_wiki":false,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":1,"forks":0,"open_issues":1,"watchers":1,"default_branch":"dev"}},"_links":{"self":{"href":"https://api.github.com/repos/thehyve/heim-SmartR/pulls/80"},"html":{"href":"https://github.com/thehyve/heim-SmartR/pull/80"},"issue":{"href":"https://api.github.com/repos/thehyve/heim-SmartR/issues/80"},"comments":{"href":"https://api.github.com/repos/thehyve/heim-SmartR/issues/80/comments"},"review_comments":{"href":"https://api.github.com/repos/thehyve/heim-SmartR/pulls/80/comments"},"review_comment":{"href":"https://api.github.com/repos/thehyve/heim-SmartR/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/thehyve/heim-SmartR/pulls/80/commits"},"statuses":{"href":"https://api.github.com/repos/thehyve/heim-SmartR/statuses/8bd3afab46cdf7653c2aa89ac3a35e2063e1bb73"}}}}