CNspector

CNSpector is a web-based browser to visualize Copy Number Variation (CNV) calls. The browser is an R program for shiny-server that reads an input file containing a table whose rows point to the files to display for a given sample or group of samples (multi-sample mode). Currently it can support output from cnvkit, copywriter and canvas tools. The outputs from these tools are converted in a format accepted by CNSpector.

Installation

Git clone the repository or download as required. The folder structure needs to remain the same to be able to run the scripts or load the references correctly.

git clone https://github.com/PapenfussLab/CNspector.git

shiny-server scripts

The following R files are provided for CNSpector browser. It was tested with R 3.3.1, 3.4.0 and 3.5.1 versions and can be launched through Rstudio.

	Helpers.R 
	Server.R
	ui.R

Reference files

The following reference files are provided to support cnv tools output conversion and for the browser in terms of annotations and bin sizes for computations –

1. annotations/browser

Required for the visualization in the browser.

  chromInfo.txt
  cytoBand.txt
  panel_transcripts.bed 
  targeted_transcripts.bed
  wg_transcripts.bed

2. annotations/preprocessing

Required for converting different tools output.

  hg19_targeted.bed
  hg19_wg_coarse.bed
  hg19_wg_fine.bed
  hg19_wg_medium.bed

<hg_19_targeted.bed/targeted_transcripts.bed/panel_transcripts.bed> - Bed files to be generated as per the panel design.

R package dependencies

Browser

The browser can be launched through Rstudio and requires the following packages to run the application correctly –

  library(futile.logger)
  library(plyr)
  library(data.table)
  library(R.utils)
  library(RColorBrewer)
  library(ggplot2)
  library(Cairo)

Conversion scripts

  library(genomation)
  library(GenomicRanges)
  library(stats)
  library(VariantAnnotation)

Convert scripts

Refer to the basic instructions provided in the documentation/CNVTools_README to help run other cnv tools (not limited to this but can be run directly by following the actual tool documentation). Conversion scripts are to convert the different tool outputs to browser acceptable input files.

1. Cnvkit

   a.	"cnvkit_output" folder needs to be placed inside the cnvkit folder. 
   b.	Run the following commands to generate the “index.tsv” file for browser
   	cd cnvkit
   	Rscript scripts/import.R 
   

2. Canvas

   a.	“canvas_output” folder needs to be location inside canvas folder.
   b.	Run the following commands to generate the CNSpector/index.tsv file for browser
   	cd canvas
   	Rscript scripts/import.R
   

3. CopyWriter

   a.	"copywriter_output" folder needs to be places inside the copywriter folder. 
   b.	Run the following commands to generate CNSpector/index.tsv file for browser.
   	cd copywriter
   	Rscript scripts/import.R
   

4. Multiple tools combination If successful running all the 3 tools, then best resolution from each tool is put together to view in the browser as follows –

   scripts/make_combination_index.sh
   Output: combination/index.tsv
   

Rstudio run Instructions

Open the server.R through Rstudio and run the application to launch the shiny application as follows –

	http://shiny.server.url/cnb/?file=<path_to_the_file.tsv>

Supported options in the URL link -

	reference_path=REFERENCE_PATH
	base_path=BASE_PATH
	run=RUN_NAME
	sample=SAMPLE_NAME
	gene_id=GENE_NAME
	locus=CHR:START-END
	debug=TRUE|FALSE
	verbose=TRUE|FALSE
	locked=TRUE|FALSE

Example to load the “index.tsv” file into the browser (specific tool / combination index )

	http://shiny.server.url/?file=prefix_path/CNspector/canvas/CNspector/index.tsv&reference_path=prefix_path/CNspector/annotations/browser&base_path=/home/canvas/CNspector

Debug mode –

	http://shiny.server.url/?file=prefix_path/CNspector/canvas/CNspector/index.tsv&reference_path=prefix_path/CNspector/annotations/browser&base_path=/home/canvas/CNspector&debug=T