AMARETTO_VisualizeModule: AMARETTO_VisualizeModule

In broadinstitute/ImagingAMARETTO: ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

Description

Function to visualize the gene modules

Usage

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

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
printHM	Boolean to print heatmap

Value

result

Examples

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/ImagingAMARETTO documentation built on Dec. 3, 2019, 6:38 p.m.