A function to plot a computed Vmat — plotVmat.default • VplotR

The default plotVmat method generates a ggplot representing a heatmap of fragment density.

# S3 method for default
plotVmat(
  x,
  hm = 90,
  colors = COLORSCALE_VMAT,
  breaks = NULL,
  xlim = c(-250, 250),
  ylim = c(50, 300),
  main = "",
  xlab = "Distance from center of elements",
  ylab = "Fragment length",
  key = "Score",
  ...
)

Arguments

x: A computed Vmat (ideally, should be normalized)
hm: Integer, should be between 0 and 100. Used to automatically scale the range of colors (best to keep between 90 and 100)
colors: a vector of colors
breaks: a vector of breaks. length(breaks) == length(colors) + 1
xlim: vector of two integers, x limits
ylim: vector of two integers, y limits
main: character, title of the plot
xlab: character, x-axis label
ylab: character, y-axis label
key: character, legend label
...: additional parameters

Value

A Vmat ggplot

Examples

data(bam_test)
data(ce11_proms)
V <- plotVmat(
    bam_test,
    ce11_proms,
    normFun = 'libdepth+nloci', 
    return_Vmat = TRUE
)
#> Computing V-mat
#> Normalizing the matrix
#> Computing raw library depth
#> Dividing Vmat by its number of loci
#> Smoothing the matrix
plotVmat(V)