plotVmat.list {VplotR} | R Documentation |
The plotVmat.GRanges() method computes and normalizes multiple Vmats before passing them to plotVmat.VmatList() method.
## 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, ... )
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:
|
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 |
A list of Vmat ggplots
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 )