oncoprint {TRONCO} | R Documentation |
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, ...)
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 |
ann.stage |
Boolean value to annotate stage classification, default depends on |
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 |
sample.id |
If TRUE shows samples name (columns). Default is FALSE |
hide.zeroes |
If TRUE trims data - see |
legend |
If TRUE shows a legend for the types of events visualized. Defualt is TRUE |
legend.cex |
Default 0.5; determines legend size if |
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 |
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 |