{"id":21089,"date":"2022-11-22T10:21:00","date_gmt":"2022-11-22T08:21:00","guid":{"rendered":"https:\/\/www.wjst.de\/blog\/?p=21089"},"modified":"2022-11-26T19:26:18","modified_gmt":"2022-11-26T17:26:18","slug":"a-r-function-creating-96-well-plate-sample-assignment","status":"publish","type":"post","link":"https:\/\/www.wjst.de\/blog\/sciencesurf\/2022\/11\/a-r-function-creating-96-well-plate-sample-assignment\/","title":{"rendered":"A R function creating 96 well plate sample assignment"},"content":{"rendered":"

Most recently I had to add forgotten data to a SQL server database that was in use only until 2010. Script language was Cold Fusion at that time creating a visual interface to 96 well plates where proband IDs are assigned to plate positions by drop down fields.<\/p>\n

R doesn’t have any good way for formatted data entry. Some shiny apps would be helpful but a bit overkill here. Data export into a javascript framework would be also a more professional solution while I just needed only a quick way to modify my database. <\/p>\n

So I came up with some R code producing html code embedding javascript functions that can export the result as SQL code, so a 4 language mixup.<\/p>\n

\"\"<\/a>
96 well plate assignment<\/figcaption><\/figure>\n
\r\ndataentry <- function(plate_id,city) {\r\n# get orig IDs from database first\r\n\r\n# position identifier A01, A02...\r\npos = NULL\r\nfor (i in 1:8) {\r\n  pos = c(pos, paste0( rep( LETTERS[i], 12), str_pad( 1:12 ,2,pad="0" ) ) )\r\n}\r\n\t\r\nHTML <- paste('<html>\r\n<script>\r\nfunction download(filename, text) {\r\n  var element = document.createElement("a");\r\n  element.setAttribute("href", "data:text\/plain;charset=utf-8," + encodeURIComponent(text));\r\n  element.setAttribute("download", filename);\r\n  element.style.display = "none";\r\n  document.body.appendChild(element);\r\n  element.click();\r\n  document.body.removeChild(element);\r\n}\r\nfunction saveValues() {\r\n  var frm = document.getElementById("f");\r\n  var params = "";\r\n  var sample_id = ',sample_id,';\r\n  for( var i=0; i<frm.length; i++ ) {\r\n    sample_id++;\r\n    var fieldId = frm.elements[i].id;\r\n    var fieldValue = frm.elements[i].value;\r\n    if (fieldValue) params += "INSERT INTO samples (plate_id,plate_position,patient_id) VALUES (',plate_id,'," + fieldId + "," + fieldValue + ")\\\\n";\r\n  }\r\n  download("',plate_id,'.SQL",params);\r\n}\r\n<\/script>\r\n<body>\r\n<form id="f">')\r\n\t\r\n# dropdowns\r\nsel ='<option value=""><\/option>'\r\nfor (i in 1:dim(patients)[1]) {\r\n  sel <- paste0(sel,'<option value=',patients[i,"patient_id"],'>',patients[i,"Orig_ID"],'<\/option>\\n')\r\n}\r\nfor (i in pos) {\r\n  if (substr(i,2,3) == "01") HTML <- paste0(HTML,'<BR>')\r\n  HTML <- paste(HTML,'<select id=',i,'>',sel,'<\/select>')\r\n}\r\n\t\r\nHTML <- paste(HTML,'<\/form>\r\n<br><input name="save" type="button" value="SQL" onclick="saveValues(); return false"\/>\r\n<\/body><\/html>')\r\n\t\r\nsink( paste('plate.html') )\r\ncat(HTML)\r\nsink()\r\n}\r\ndataentry(725,'city')\r\n<\/pre>\n\n
 <\/p>\n
\n  CC-BY-NC Science Surf , accessed 03.04.2026<\/span>\n <\/div>","protected":false},"excerpt":{"rendered":"
Most recently I had to add forgotten data to a SQL server database that was in use only until 2010. Script language was Cold Fusion at that time creating a visual interface to 96 well plates where proband IDs are assigned to plate positions by drop down fields. R doesn’t have any good way for … Continue reading A R function creating 96 well plate sample assignment<\/span> →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[9],"tags":[3989,2893,3986,3988,3987,3983,2823,1863,2771],"class_list":["post-21089","post","type-post","status-publish","format-standard","hentry","category-computer-software","tag-96-well-plate","tag-r","tag-sql","tag-biology","tag-data-entry","tag-dropdown","tag-html","tag-interface","tag-javascript"],"_links":{"self":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/21089","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/comments?post=21089"}],"version-history":[{"count":8,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/21089\/revisions"}],"predecessor-version":[{"id":21155,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/21089\/revisions\/21155"}],"wp:attachment":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/media?parent=21089"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/categories?post=21089"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/tags?post=21089"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}