plotVmat.list: A function to compute (and plot) several Vmats.

In js2264/VplotR: Set of tools to make V-plots and compute footprint profiles

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
)

js2264/VplotR documentation built on Jan. 4, 2024, 7:49 p.m.