p2ViewPagodaApp {pagoda2}

p2ViewPagodaApp R6 class

Description

Modified 'PAGODA1' app (from 'SCDE') for browsing 'pagoda2' results. Refer to 'ViewPagodaAppOld' and 'make.pagoda.app()' in 'SCDE'

Public fields

results

Result object returned by scde.expression.difference() (default=NULL). Note to browse group posterior levels, use return.posteriors = TRUE in the scde.expression.difference() call.

type

Either 'counts' or a name of a 'reduction' in the 'Pagoda2' object

genes

List of genes to display in the Detailed clustering panel (default=list())

batch

Any batch or other known confounders to be included in the visualization as a column color track (default=NULL)

pathways

character vector Pathway or gene names (default=NULL)

name

App name (needs to be altered only if adding more than one app to the server using the 'server' parameter) (default=NULL)

trim

Trim quantity used for Winsorization for visualization

embedding

Embedding information (default=NULL)

veloinfo

Velocity information (default=NULL)

goenv

environment mapping pathways to genes (default=NULL)

renv

Global environment (default=NULL)

Methods

Public methods

• p2ViewPagodaApp$new()

• p2ViewPagodaApp$getgenecldata()

• p2ViewPagodaApp$call()

• p2ViewPagodaApp$clone()

Method new()

Initialize p2ViewPagodaApp class

Usage

p2ViewPagodaApp$new(
  results,
  pathways,
  genes,
  goenv,
  batch = NULL,
  name = "pathway overdispersion",
  trim = 1.1/nrow(p2$counts),
  embedding = NULL,
  type,
  veloinfo = NULL
)

Arguments

results

Result object returned by scde.expression.difference(). Note to browse group posterior levels, use return.posteriors = TRUE in the scde.expression.difference() call.

pathways

character vector Pathway or gene names (default=NULL)

genes

list Genes to display in the Detailed clustering panel (default=list())

goenv

Environment mapping pathways to genes (default=NULL)

batch

Any batch or other known confounders to be included in the visualization as a column color track (default=NULL)

name

string App name (needs to be altered only if adding more than one app to the server using the 'server' parameter) (default="pathway overdispersion")

trim

numeric Trim quantity used for Winsorization for visualization (default=1.1/nrow(p2$counts) whereby the 'counts' from the 'Pagoda2' object is the gene count matrix, normalized on total counts (default=NULL)

embedding

Embedding information (default=NULL)

type

Either 'counts' or a name of a 'reduction' in the 'pagoda2' object

veloinfo

Velocity information (default=NULL)

Returns

new 'p2ViewPagodaApp' object

Method getgenecldata()

Helper function to get the heatmap data for a given set of genes

Usage

p2ViewPagodaApp$getgenecldata(genes = NULL, gcl = NULL, ltrim = 0)

Arguments

genes

character vector Gene names (default=NULL)

gcl

pathway or gene-weighted PCA (default=NULL). If NULL, uses tp2c.view.pathways(self$genes, self$results$p2, goenv=goenv, vhc=self$results$hvc, plot=FALSE, trim=ltrim, n.genes=Inf).

ltrim

numeric Winsorization trim that should be applied (default=0)

Returns

heatmap data for a given set of genes

Method call()

Call Rook application. Using client-side ExtJS framework and Inchlib HTML5 canvas libraries to create the graphical user interface for PAGODA

Usage

p2ViewPagodaApp$call(env)

Arguments

env

The environment argument is a true R environment object which the application is free to modify. Please see the Rook documentation for more details.

Returns

modified 'PAGODA1' app

Method clone()

The objects of this class are cloneable with this method.

Usage

p2ViewPagodaApp$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.