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Code Book

Jasmine Dumas edited this page May 11, 2015 · 4 revisions

A detailed explanation of variables used within this application. This is a nod taken from the Jeff Leek Group Guide to Sharing Data - This is a pillar of reproducible research and aims to enhance scientific comprehension.


Application Layout

  1. ui.r: The user-interface (ui) script controls the layout and appearance of the app. For readability the current GEO-AWS app houses the source scripts for sidebarPanel.R, and the mainPanel.R only, which forms a fluid page for the side bar panel and the main panel which consists of tabs with clinical data and graphical analyses.
  2. server.r: The server.R script contains the instructions that the computer needs to build the app. The current GEO-AWS houses the source scripts for stripchart2.R, server-reactives.R, server-output.R. This comprises of our visualization of gene expression across our clinical variables, our reactives which update as we change our parameters in the side panel, and our server output.
  3. stripchart2.R: A function that dictates the the look and paramters (jitter, coloring, etc) of the GEO-AWS graph.
  4. server-reactives.R: Our reactive functions that power our app and our selections.
  5. server-output.R: Includes our display functions for conditional panels, Renders drop-down menu for variables, function to select most recent item selected, Renders drop-down menu for levels, callback "Click" parameter for selecting rows in our clinical data frame/summary, and displays the Clinical Data Table.
  6. mainPanel.R: Conditional displays initial directions on how to use the application, tab panels which include info such as information about the authors (research students), and processing-please wait message/graphic
  7. sidebarPanel.R: input widgets for: entering the GEO number, conditional display of platforms for selections, conditional display of server-side generated: Genes, Probes, Columns, and Groups

Reactives

Functions

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