oncoprint: oncoprint
In BIMIB-DISCo/TRONCO: TRONCO, an R package for TRanslational ONCOlogy

oncoprint

R Documentation

oncoprint

Description

oncoPrint : plot a genotype. For details and examples regarding the visualization through oncoprints, we refer to the Vignette Section 4.4.

Usage

oncoprint(
  x,
  excl.sort = TRUE,
  samples.cluster = FALSE,
  genes.cluster = FALSE,
  file = NA,
  ann.stage = has.stages(x),
  ann.hits = TRUE,
  stage.color = "YlOrRd",
  hits.color = "Purples",
  null.color = "lightgray",
  border.color = "white",
  text.cex = 1,
  font.column = NA,
  font.row = NA,
  title = as.description(x),
  sample.id = FALSE,
  hide.zeroes = FALSE,
  legend = TRUE,
  legend.cex = 0.5,
  cellwidth = NA,
  cellheight = NA,
  group.by.label = FALSE,
  group.by.stage = FALSE,
  group.samples = NA,
  gene.annot = NA,
  gene.annot.color = "Set1",
  show.patterns = FALSE,
  annotate.consolidate.events = FALSE,
  txt.stats = paste(nsamples(x), " samples\n", nevents(x), " events\n", ngenes(x),
    " genes\n", npatterns(x), " patterns", sep = ""),
  gtable = FALSE,
  ...
)

Arguments

`x`	A TRONCO compliant dataset
`excl.sort`	Boolean value, if TRUE sorts samples to enhance exclusivity of alterations
`samples.cluster`	Boolean value, if TRUE clusters samples (columns). Default FALSE
`genes.cluster`	Boolean value, if TRUE clusters genes (rows). Default FALSE
`file`	If not NA write to `file` the Oncoprint, default is NA (just visualization).
`ann.stage`	Boolean value to annotate stage classification, default depends on `x`
`ann.hits`	Boolean value to annotate the number of events in each sample, default is TRUE
`stage.color`	RColorbrewer palette to color stage annotations. Default is 'YlOrRd'
`hits.color`	RColorbrewer palette to color hits annotations. Default is 'Purples'
`null.color`	Color for the Oncoprint cells with 0s, default is 'lightgray'
`border.color`	Border color for the Oncoprint, default is white' (no border)
`text.cex`	Title and annotations cex, multiplied by font size 7
`font.column`	If NA, half of font.row is used
`font.row`	If NA, max(c(15 * exp(-0.02 * nrow(data)), 2)) is used, where data is the data visualized in the Oncoprint
`title`	Oncoprint title, default is as.name(x) - see `as.name`
`sample.id`	If TRUE shows samples name (columns). Default is FALSE
`hide.zeroes`	If TRUE trims data - see `trim` - before plot. Default is FALSE
`legend`	If TRUE shows a legend for the types of events visualized. Defualt is TRUE
`legend.cex`	Default 0.5; determines legend size if `legend = TRUE`
`cellwidth`	Default NA, sets autoscale cell width
`cellheight`	Default NA, sets autoscale cell height
`group.by.label`	Sort samples (rows) by event label - usefull when multiple events per gene are available
`group.by.stage`	Default FALSE; sort samples by stage.
`group.samples`	If this samples -> group map is provided, samples are grouped as of groups and sorted according to the number of mutations per sample - usefull when `data` was clustered
`gene.annot`	Genes'groups, e.g. list(RAF=c('KRAS','NRAS'), Wnt=c('APC', 'CTNNB1')). Default is NA.
`gene.annot.color`	Either a RColorColorbrewer palette name or a set of custom colors matching names(gene.annot)
`show.patterns`	If TRUE shows also a separate oncoprint for each pattern. Default is FALSE
`annotate.consolidate.events`	Default is FALSE. If TRUE an annotation for events to consolidate is shown.
`txt.stats`	By default, shows a summary statistics for shown data (n,m, \|G\| and \|P\|)
`gtable`	If TRUE return the gtable object
`...`	other arguments to pass to pheatmap