Goal: Learn More About Cancer for Clues To Effective Treatment. Research is often an exploration

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Sabrina Barnett
5 years ago
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1 The Project

2 Goal: Learn More About Cancer for Clues To Effective Treatment Research is often an exploration Look for trends in cancer occurrences Look for trends in treatments Perhaps something will pop out that will suggest a new approach to a cure, or an early detection strategy

3 Real Data, Real Questions Dr. Prasad has given us some clinical data to explore Cancer Patients summary: Approximately 100 subjects in study 10 types of cancer found age range 2 88 Received gamma knife treatment Data Fields patient_id birthdate gende r diagnosis treatments targets shots

4 Real Questions 1. Display Age distribution by diagnosis 2. Display gender distribution by diagnosis 3. For Diagnosis "Metastasis Multiple": How many targets treated per patient? 4. For diagnosis "Acoustic Schwannoma": How many shots were used per patient? 5. Display Ages of Cancer Patients: at what age is the most frequent occurrence?

5 Time Permitting: Table Characteristic No. of Patients No. of Lesions (targets) Age > 50 Age <= 50 Male Female 1 treatment Patient Population in [Number of Patients] Cases > 1 treatment Single Metastasis Multiple Metastasis

6 What will the answers look like??? 1. Display Age distribution by diagnosis 2. Display gender distribution by diagnosis 3. For Diagnosis "Metastasis Multiple": How many targets treated per patient? 4. For diagnosis "Acoustic Schwannoma": How many shots were used per patient? 5. Display Ages of Cancer Patients patient_id birthdate gende r diagnosis treatments targets shots

7 Your Mission (should you choose to accept it) Write php code to parse the data and find the answers The answers will be a bunch of numbers, so.. Use charts to visualize the answers Display in a web page so that the results can be shared with other scientists

8 But php doesn t draw charts So we need another web page language, javascript Don t panic! There is a javascript library of functions to draw charts named jqplot (which uses jquery) So first we need to include those library files in the html part of our php files Similar idea to require_once( filename ) for php

9 Javascript Javascript files are loaded before the body of the html document in the head <html> <head>  <link rel="stylesheet" type="text/css" href="js/jquery.jqplot.css" /> <link rel="stylesheet" type="text/css" href="js/examples.css" />  <script language="javascript" type="text/javascript" src="js/jquery min.js"></script>   <script language="javascript" type="text/javascript" src="js/jquery.jqplot.js"></script> <script language="javascript" type="text/javascript" src="js/plugins/jqplot.barrenderer.js"></script> <script language="javascript" type="text/javascript" src="js/plugins/jqplot.categoryaxisrenderer.js"></script> <script language="javascript" type="text/javascript" src="js/plugins/jqplot.highlighter.js"></script> <script language="javascript" type="text/javascript" src="js/plugins/jqplot.pointlabels.js"></script> <script language="javascript" type="text/javascript" src="js/plugins/jqplot.canvastextrenderer.min.js"></script> <script language="javascript" type="text/javascript" src="js/plugins/jqplot.canvasaxislabelrenderer.min.js"></script> <script language="javascript" type="text/javascript" src="js/plugins/jqplot.canvasaxistickrenderer.min.js"></script> <!-- END: load jqplot </head><body> <?php?> </body> </html>

10 Code that writes code We provide you a function that generates javascript to draw a bar chart Use require_once to get the function Make a function call whenever you need it. <?php require_once('drawchart.php'); // $bardata and X_tic_labels are arrays // maxytick is a number // the rest of the parameters are strings drawchart( $bardata, $X_tic_labels, $max_y_tick, $charttitle, $yaxislabel,$xaxislabel);

11 Dealing With Data Data is a file of tab separated values patient_id birthdate gender diagnosis treatments targets m Metastasis Single m Pituitary Adenoma 1 1 We will convert this to an array of rows. Each row will be an associative array 0 (patient_id =>1, birthdate => , gender =>m, ) 1 (patient_id =>2, birthdate => , gender =>m, ) Use a foreach loop to go through rows Use associativity to get a field

12 Dealing With Data 0 (patient_id =>1, birthdate => , gender =>m, ) 1 (patient_id =>2, birthdate => , gender =>m, ) foreach($data_array as $key =>$rowarray){ // one patient s record if($rowarray['gender'] == "m") { // do something } }

13 Useful functions parsecsv($filename, $delimiter) min($myarray) max($myarray) count($myarray) print_r($myarray) Please use your own average function stdev your own or shared from another group

14 Histograms A histogram is a graph displaying frequencies, displayed by bars. They are used to roughly estimate probability distribution of a variable by showing the frequencies within ranges of values. Histogram buckets are buckets of data, each with a range of values (like 0 5).

15 Histogram Bucket Example Data- 3, 11, 8, 1, 4,13

16 Let s give it a try!

Date Picker Haim Michael

Date Picker Haim Michael Date Picker Introduction The date picker is one of the most popular jquery widgets in use. It is highly configurable and extremely easy to implement. Introduction Simple Date Picker