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