rainfallBQ: kataegis plot for a single TCGA sample

In teamcgc/cgcR: NCI Cancer Genomics Cloud examples in R

Description

kataegis plot for a single TCGA sample: mutation types are scatterplotted in genomic coordinates with altitude of points measuring proximity in genomic coordinates to neighbor

Usage

rainfallBQ(bq, studytag = "LUAD", VariantType = "SNP", id = "TCGA-05-4398", 
   colmap = kataColors(), 
   ymax = 9, inylab = "-log10 dbp", inxlab = "chromosome", 
   intitle, dotrim = TRUE, addbounds = TRUE, cnames = TRUE)

Arguments

bq	a src\_bigquery instance
studytag	alphabetic short code for TCGA tumor type, e.g, LUAD for lung adenocarcinoma, OV for ovarian cystadenocarcinoma, etc.
VariantType	code for type of variant, currently SNP is all that is expected
id	a ParticipantBarcode value for selected study
colmap	vector map from mutation code to colors
ymax	maximum altitude of points
inylab	label for y axis – will be -log10dbp to indicate -log10 distance in base pairs to nearest mutation
inxlab	label for x axis
intitle	graph title
addbounds	logical: if TRUE add some space at ends of x axis
cnames	logical: if TRUE add chromosome names

Details

uses ggplot2 to plan a visualization of mutation density, genome-wide

note that if addbounds and cnames are set to false, the resulting gg instance can in principle be made interactive with ggplotly

Value

ggplot instance

Author(s)

VJ Carey <[e-mail]>

References

Alexandrov, Ludmil B Nik-Zainal, Serena Wedge, David C et al., Signatures of mutational processes in human cancer, Nature 2013.

Examples

 ## Not run: 
  # get a bigquery instance in bq
  rainfallBQ(bq)
 
## End(Not run)

teamcgc/cgcR documentation built on May 31, 2019, 7:56 a.m.