AMARETTO_VisualizeModule: AMARETTO_VisualizeModule

Description Usage Arguments Value Examples

View source: R/amaretto_vizualize.R

Description

Function to visualize the gene modules

Usage

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AMARETTO_VisualizeModule(AMARETTOinit, AMARETTOresults, ProcessedData,
  ModuleNr, show_row_names = FALSE, SAMPLE_annotation = NULL,
  ID = NULL, order_samples = NULL)

Arguments

AMARETTOinit

List output from AMARETTO_Initialize().

AMARETTOresults

List output from AMARETTO_Run().

ProcessedData

List of processed input data

ModuleNr

Module number to visualize

show_row_names
SAMPLE_annotation

Matrix or Dataframe with sample annotation

ID

Column used as sample name

order_samples

Order samples in heatmap by mean or by clustering

Value

result

Examples

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data('ProcessedDataLIHC')
AMARETTOinit <- AMARETTO_Initialize(ProcessedData = ProcessedDataLIHC,
                                    NrModules = 2, VarPercentage = 50)

AMARETTOresults <- AMARETTO_Run(AMARETTOinit)

AMARETTO_VisualizeModule(AMARETTOinit = AMARETTOinit,AMARETTOresults = AMARETTOresults,
                         ProcessedData = ProcessedDataLIHC, ModuleNr = 1)

broadinstitute/PerturbationAMARETTO documentation built on Nov. 4, 2019, 8:14 a.m.