v_Circos: Main function for module: Circos

In yilixu/vigilante: Visualizing Integrated Genomics in Linked and Nested Translational Elaboration & Knowing Numbers in Genomic Hypothesis Through Statistics

Description

Extract, clean and reform NGS data, and then generate comprehensive Circos plot with each track (circle) representing different types of data. Currently supported tracks: BAF (B allele frequency), CNA (copy number alterations), mutation burden (somatic/germline mutations), gene expression (TPM) and gene fusions (cross-check validation is available when 2 or more fusion callers are in use; also, fusion status check and validation through statistics are available via module CSE).

Usage

v_Circos(
  outputFolderPath = "./_VK/_Circos/",
  startNum = NULL,
  endNum = NULL,
  customPlotNum = NULL,
  doBAF = FALSE,
  doCNA = FALSE,
  doMB = c(FALSE, "somatic", "germline"),
  doGE = c(FALSE, "log"),
  doFL = FALSE
)

Arguments

outputFolderPath	string, relative or absolute path to the output folder, trailing slash "/" required, can be set to NULL (no output file will be written to the file system), default "./_VK/_Circos/" for module Circos.
startNum	integer, by default, vigilante will go through every individual sample and sample group, generating a Circos plot per each item in the list. If an integer is specified, vigilante will instead start generating Circos plots at the specified index (e.g. there 10 samples and 2 groups in the list, set startNum to 11 will make vigilante start generating Circos plots at the first group). If set to NULL, vigilante will automatically detect Circos pltos already existing in the output folder and continue at the most recent generated one (e.g. there are 12 Circos plots in total to be generated and 6 of them already exist in the output folder, to make sure all plots are fully-rendered, vigilante will continue at the 6th plot and overwrite it). Since generating comprehensive Circos plots is very computational-intensive, it is possible that function runs get interrupted and half-rendered plots get generated because of running out of memory. Therefore, it is recommended to set startNum to NULL so that vigilante can ensure every item in the list to be plotted get fully-rendered.
endNum	integer, by default, vigilante will go through every individual sample and sample group, generating a Circos plot per each item in the list. If an integer is specified, vigilante will instead stop generating Circos plots at the specified index (e.g. there 10 samples and 2 groups in the list, set endNum to 6 will make the 6th sample as the last one to be plotted, and there will be no Circos plots for items after the 6th sample).
customPlotNum	integer vector, optional, can be set to NULL; if provided, will override "startNum" and "endNum", and only Circos plots at the specified index will be generated (e.g. there 10 samples and 2 groups in the list, set customPlotNum to c(3, 11) will make only the 3rd sample and the 1st group to be plotted).
doBAF	logic, whether to show BAF track on Circos plots.
doCNA	logic, whether to show CNA track on Circos plots.
doMB	mixed vector, c(FALSE, "somatic", "germline"), whether to show MB track on Circos plots; if TRUE, specify the mutation type, can be either "somatic" or "germline" or both, each type will be shown as a separate track on Circos plots.
doGE	mixed vector, c(FALSE, "log"), whether to show GE track on Circos plots; if TRUE, specify the value format, can be either "log" or "TPM", choose "TPM" for showing raw TPM value, choose "log" for showing value after log10 conversion (0 will be converted into negative value based on the value range across all samples), must match the value format chosen in v_prepareVdata_Circos function.
doFL	logic, whether to show FL track will be shown on Circos plots.

Details

Please be aware that generating comprehensive Circos plots may become very computational-intensive and time-consuming depending on input data, and it is possible that function runs get interrupted and half-rendered plots get generated because of running out of memory. But no need to worry, vigilante has already taken this possible issue into consideration and come with an internal mechanism to help minimize the interruption. Please see the description of argument "startNum" and properly set it to better utilize the interal helper mechanism.

Value

NULL, when a valid outputFolderPath is provided, output Circos plots will be generated and saved in the provided location, otherwise function run will stop and nothing will be written into the file system.

yilixu/vigilante documentation built on June 4, 2021, 5:07 a.m.