cnvPlot

This function is used for drawing diagram and scatter plot for each sample.

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

cnvPlot(cnsInput=None, cnrInput=None,
        outputdir=None, diagram=True,
        diagram_params={"--threshold": 0.5, "--min-probes": 3, "-y": True},
        scatter=True,
        scatter_params={"--y-max": 2, "--y-min": -2, "--segment-color": "'red'"},
        threads=1, stepNum=None, upstream=None,
        verbose=False, **kwargs)

  • cnsInput: list, cns files(copy number segments), generating from cnvkit.py batch.

  • 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.

  • threads: int, how many thread to use.

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

  • diagram_params: dict, parameter for cnvkit.py breaks, default is {“–threshold”: 0.5, “–min-probes”: 3, “-y”: True}

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

  • scatter_params: dict, parameter for cnvkit.py scatter, default is {“–y-max”: 2, “–y-min”: -2, “–segment-color”: “‘red’”}

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

  • verbose: bool, True means print all stdout, but will be slow; False means black stdout verbose, much faster.

  • 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",
 )