plotVmat.list {VplotR} | R Documentation

## A function to compute (and plot) several Vmats.

### Description

The plotVmat.GRanges() method computes and normalizes multiple Vmats before passing them to plotVmat.VmatList() method.

### Usage

    ## S3 method for class 'list'
    plotVmat(
      x,
      cores = 1,
      cores_subsetting = 1,
      nrow = NULL,
      ncol = NULL,
      xlims = c(-250, 250),
      ylims = c(50, 300),
      normFun = "libdepth+nloci",
      s = 0.95,
      roll = 3,
      return_Vmat = FALSE,
      verbose = 1,
      ...
    )

### Arguments

`x` | list Each element of the list should be a list containing paired-end fragments and GRanges of interest.
`cores` | Integer, number of cores to parallelize the plots
`cores_subsetting` | Integer, number of threads to parallelize fragments subsetting
`nrow` | Integer, how many rows in facet?
`ncol` | Integer, how many cols in facet?
`xlims` | x limits of the computed Vmat
`ylims` | y limits of the computed Vmat
`normFun` | character. A Vmat should be scaled either by: 'libdepth+nloci', e.g. the library depth and the number of loci used to compute the Vmat; zscore, if relative patterns of fragment density are more important than density per se; Alternatively, the Vmat can be scaled to a chosen quantile ('quantile') or to the max Vmat value ('max').
`s` | A float indicating which quantile to use if 'quantile' normalization is chosen
`roll` | integer, to use as the window to smooth the Vmat rows by rolling mean.
`return_Vmat` | Boolean, should the function return the computed Vmat rather than the plot?
`verbose` | Boolean
`...` | additional parameters

### Value

A list of Vmat ggplots

### Examples

    data(bam_test)
    data(ce11_proms)
    list_params <- list(
        'germline' = list(
            bam_test,
            ce11_proms[ce11_proms$which.tissues == 'Germline']
        ),
        'muscle' = list(
            bam_test,
            ce11_proms[ce11_proms$which.tissues == 'Muscle']
        )
    )
    V <- plotVmat(
        list_params,
        normFun = 'libdepth+nloci',
        roll = 5
    )

[Package VplotR version 1.4.0 Index]