cnvHeatmap

This function is used for drawing heatmap plot including all samples.

Note

This function is calling cnvkit.py batch, please install cnvkit before using.

cnvkit official docs

Talevich, Eric, et al. “CNVkit: genome-wide copy number detection and visualization from targeted DNA sequencing.” PLoS computational biology 12.4 (2016): e1004873.

Parameters

cnvHeatmap(cnrInput=None,
           outputdir=None, orderfile=None,
           other_params={"-d": True, "-y": True},
           stepNum=None, upstream=None, **kwargs)

  • cnrInput: list, cnr files( a table of copy number ratios), generating from cnvkit.py batch.

  • outputdir: str, output result folder, None means the same folder as input files.

  • orderfile: str, a file contain the cnr file name to reorder the outfile, you can miss this parameter which will ordered as the cnrInput.

  • diagram: True, drawing diagram plot? default is True.

  • other_params: dict, parameter for cnvkit.py heatmap, default is {{“-d”: True, “-y”: True}. other parameter could setting as this {“-c”: “chr8”} as for designate chromosome. {“-g”: “EXT1,PXDNL”} is for designate gene analysis.

  • stepNum: int or str, step flag for folder name.

  • upstream: upstream output results, used for cnv pipeline, just can be cnvbatch. This parameter can be True, which means a new pipeline start.

Warning

We recommend using this function in bin-level CNV detection.

Example usage:

 from cfDNApipe import *
 import glob

 pipeConfigure(
     threads=60,
     genome="hg19",
     refdir=r"path_to_reference/hg19",
     outdir=r"path_to_output/snv_output",
     data="WGS",
     type="paired",
     build=True,
     JavaMem="10G",
 )

bams = ["test1.bam", "test1.bam"]
verbose = True

 res_cnvbatch = cnvbatch(
     casebamInput=bams,
     caseupstream=True,
     access=Configure.getConfig("access-mappable"),
     annotate=Configure.getConfig("refFlat"),
     verbose=verbose,
     stepNum="CNV01",
 )
 res_cnvPlot = cnvPlot(upstream=res_cnvbatch, verbose=verbose, stepNum="CNV02",)
 res_cnvTable = cnvTable(
     upstream=res_cnvbatch, verbose=verbose, stepNum="CNV03",
 )
 res_cnvHeatmap = cnvHeatmap(
     upstream=res_cnvbatch, verbose=verbose, stepNum="CNV04",
 )