ViewPagodaApp-class {scde} | R Documentation

## A Reference Class to represent the PAGODA application

### Description

This ROOK application class enables communication with the client-side ExtJS framework and Inchlib HTML5 canvas libraries to create the graphical user interface for PAGODA Refer to the code in `make.pagoda.app` for usage example

### Fields

`results`

  Output of the pathway clustering and redundancy reduction

`genes`

  List of genes to display in the Detailed clustering panel

`mat`

  Matrix of posterior mode count estimates

`matw`

  Matrix of weights associated with each estimate in `mat`

`goenv`

  Gene set list as an environment

`renv`

  Global environment

`name`

  Name of the application page; for display as the page title

`trim`

  Trim quantity used for Winsorization for visualization

`batch`

  Any batch or other known confounders to be included in the visualization as a column color track

[Package scde version 2.8.0 Index]