CELLector.changeSScolors: Changing CELLector searching space color scheme

In najha/CELLector: Genomics guided selection of cancer cell lines

Changing CELLector searching space color scheme

Description

This function reassigns a set of distinc random colors to the cancer patients' subtypes identified and stored in the CELLector searching space (compute by the CELLector.Build_Search_Space function). These colors are used by the visualisation functions CELLector.visualiseSearchingSpace and CELLector.visualiseSearchingSpace_sunBurst

Usage

CELLector.changeSScolors(searchSpace)

Arguments

searchSpace

A CELLector searching space as returned by the CELLector.Build_Search_Space function

Value

A CELLector searching space as returned by the CELLector.Build_Search_Space function, with new colors

Author(s)

Hanna Najgebauer and Francesco Iorio

See Also

CELLector.Build_Search_Space,

CELLector.Build_Search_Space,

CELLector.visualiseSearchingSpace_sunBurst

Examples

data(CELLector.PrimTum.BEMs)
data(CELLector.Pathway_CFEs)
data(CELLector.CFEs.CNAid_mapping)
data(CELLector.CFEs.CNAid_decode)
data(CELLector.HCCancerDrivers)
data(CELLector.CellLine.BEMs)


tumours_BEM<-CELLector.PrimTum.BEMs$COREAD
CELLlineData<-CELLector.CellLine.BEMs$COREAD

### unicize the sample identifiers for the tumour data
tumours_BEM<-CELLector.unicizeSamples(tumours_BEM)

### building the CELLector searching space
CSS<-CELLector.Build_Search_Space(ctumours = t(tumours_BEM),
                                  verbose = FALSE,
                                  minGlobSupp = 0.05,
                                  cancerType = 'COREAD',
                                  pathway_CFEs = CELLector.Pathway_CFEs,
                                  cnaIdMap = CELLector.CFEs.CNAid_mapping,
                                  mutOnly = FALSE,
                                  cnaIdDecode = CELLector.CFEs.CNAid_decode,
                                  cdg = CELLector.HCCancerDrivers)

### visualising the Searching space as collapsible tree
CELLector.visualiseSearchingSpace(searchSpace = CSS,CLdata = CELLlineData)
### visualising the Searching space as sunburst
CELLector.visualiseSearchingSpace_sunBurst(searchSpace = CSS)

### changing the searching space colors
CSS<-CELLector.changeSScolors(CSS)

### visualising the Searching space as collapsible tree
CELLector.visualiseSearchingSpace(searchSpace = CSS,CLdata = CELLlineData)
### visualising the Searching space as sunburst
CELLector.visualiseSearchingSpace_sunBurst(searchSpace = CSS)

najha/CELLector documentation built on Sept. 4, 2024, 10:17 p.m.