## ----include=FALSE------------------------------------------------------------ library(TRONCO) data(aCML) data(crc_maf) data(crc_gistic) data(crc_plain) ## ----------------------------------------------------------------------------- dataset = rename.gene(aCML, 'TET2', 'new name') dataset = rename.type(dataset, 'Ins/Del', 'new type') as.events(dataset, type = 'new type') ## ----------------------------------------------------------------------------- dataset = join.events(aCML, 'gene 4', 'gene 88', new.event='test', new.type='banana', event.color='yellow') ## ----------------------------------------------------------------------------- dataset = join.types(dataset, 'Nonsense point', 'Nonsense Ins/Del') as.types(dataset) ## ----------------------------------------------------------------------------- dataset = delete.gene(aCML, gene = 'TET2') dataset = delete.event(dataset, gene = 'ASXL1', type = 'Ins/Del') dataset = delete.samples(dataset, samples = c('patient 5', 'patient 6')) dataset = delete.type(dataset, type = 'Missense point') view(dataset) ## ----------------------------------------------------------------------------- dataset = samples.selection(aCML, samples = as.samples(aCML)[1:3]) view(dataset) ## ----------------------------------------------------------------------------- dataset = events.selection(aCML, filter.freq = .05, filter.in.names = c('EZH1','EZH2'), filter.out.names = 'SETBP1') ## ----------------------------------------------------------------------------- as.events(dataset) ## ----fig.width=7, fig.height=5.5, fig.cap="Multiple output from oncoprint can be captured as a gtable and composed via grid.arrange (package gridExtra). In this case we show aCML data on top -- displayed after the as.alterations transformation -- versus a selected subdataset of events with a minimum frequency of 5%, force exclusion of SETBP1 (all events associated), and inclusion of EZH1 and EZH2.", results='hide'---- library(gridExtra) grid.arrange( oncoprint(as.alterations(aCML, new.color = 'brown3'), cellheight = 6, cellwidth = 4, gtable = TRUE, silent = TRUE, font.row = 6)$gtable, oncoprint(dataset, cellheight = 6, cellwidth = 4, gtable = TRUE, silent = TRUE, font.row = 6)$gtable, ncol = 1)