oncoPrint: oncoPrint
In ahmetz/oncoPrintr: Create oncoPrints Based on Genomic Data

Description Usage Arguments Value Examples

View source: R/oncoPrint.R

This function creates onco prints of genomic data based on mutations, copy number alterations, fusions, and other user defined categories. For each category 3 fields are required : Sample ID, Gene, and Variant Class. There are options to display binary events as well as continous variables.

oncoPrint(data = NULL, sort = TRUE, convert = TRUE,
  total_samples = NULL, geneName = NULL, annotation = NULL,
  annotation_order = NULL, continuous_data = NULL,
  categorical_data = NULL, categorical_data_colors = NULL,
  onco_colors = list(Mutation = "#26A818", Missense = "#26A818", Nonsense =
  "black", Splicing = "#ffaa00", Frameshift = "#A05E35", Promoter = "#2986E2",
  InFrame = "#F26529", Present = "darkorchid2", NotPresent = "#DCD9D3",
  NotTested = "darkgrey", del = "red", LOH = "#D17878", homodel = "brown4",
  CNLOH = "deepskyblue", Amplification = "#EA2E49", Deletion = "#174D9D", Yes =
  "#155B6B", No = "#12C8F9", Unknown = "azure1", Fusion = "#D38C1F", Pathogenic
  = "white"), alteration_score = list(Amplification = 5, Fusion = 4.5,
  Deletion = 4, Pathogenic = 3, Nonsense = 2.8, Frameshift = 2.6, Splicing =
  2.5, InFrame = 2, Promoter = 2, Mutation = 1, Missense = 1, Present = 1,
  NotTested = 0, None = 0, NotPresent = 0, Yes = 0, No = 0, del = 3, homodel =
  2, LOH = 1.5, CNLOH = 1), printSamples = F, xpadding = 0.1,
  ypadding = 0.1)

`data`	A list of dataframes to be included in the oncoprint. For each data frame required columns are: Sample, Gene, Variant Type
`sort`	Boelean indicating whether genes should be sorted or now (default: True)
`convert`	Boelean indicating whether varclasses should be converted to more standard names (default: True)
`total_samples`	Total number of samples. If not given, total row numbers of input will be used
`geneName`	If given, genes are not automatically sorted. Instead this variable is used for sorting. Partial list of genes can be input
`annotation_order`	This is the order of annotation categories to display. Required if annotations are given
`alteration_score`	this list determines the relative importance of different genomic alterations. Amplification > Deletion > Mutations etc.
`printSamples`	Bolean indicating whether sample names should be printed under the oncoprint
`xpadding`	numerical value of the padding between two consecutive data columns
`ypadding`	numerical value of the padding between two consecutive data rows
`annotations`	If given, these will be used for creating sub-groups of samples. Clustering will happen within annotatoion groups and then merged