p2ViewPagodaApp | R Documentation |
Modified 'PAGODA1' app (from 'SCDE') for browsing 'pagoda2' results. Refer to 'ViewPagodaAppOld' and 'make.pagoda.app()' in 'SCDE'
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)
new()
Initialize p2ViewPagodaApp class
p2ViewPagodaApp$new( results, pathways, genes, goenv, batch = NULL, name = "pathway overdispersion", trim = 1.1/nrow(p2$counts), embedding = NULL, type, veloinfo = NULL )
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$counts) whereby the 'counts' from the 'Pagoda2' object is the gene count matrix, normalized on total counts (default=NULL)
embedding
Embedding information (default=NULL)
type
Either 'counts' or a name of a 'reduction' in the 'pagoda2' object
veloinfo
Velocity information (default=NULL)
new 'p2ViewPagodaApp' object
getgenecldata()
Helper function to get the heatmap data for a given set of genes
p2ViewPagodaApp$getgenecldata(genes = NULL, gcl = NULL, ltrim = 0)
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$hvc, plot=FALSE, trim=ltrim, n.genes=Inf).
ltrim
numeric Winsorization trim that should be applied (default=0)
heatmap data for a given set of genes
call()
Call Rook application. Using client-side ExtJS framework and Inchlib HTML5 canvas libraries to create the graphical user interface for PAGODA
p2ViewPagodaApp$call(env)
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.
modified 'PAGODA1' app
clone()
The objects of this class are cloneable with this method.
p2ViewPagodaApp$clone(deep = FALSE)
deep
Whether to make a deep clone.
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