oncoprint {TRONCO} | 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

[Package TRONCO version 2.24.0 Index]