ViewPagodaApp-class: A Reference Class to represent the PAGODA application

In hms-dbmi/scde: Single Cell Differential Expression

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

hms-dbmi/scde documentation built on April 19, 2023, 10:21 p.m.