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Code Book
Jasmine Dumas edited this page May 11, 2015
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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.
- 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.
- 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.
- stripchart2.R: A function that dictates the the look and paramters (jitter, coloring, etc) of the GEO-AWS graph.
- server-reactives.R: Our reactive functions that power our app and our selections.
- 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.
- 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
- 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