oncoprint — oncoprint • TRONCO

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

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