plotVmat.default {VplotR} | R Documentation

## A function to plot a computed Vmat

### Description

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

### Usage

    ## Default S3 method:
    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
    )
    plotVmat(V)

[Package VplotR version 1.4.0 Index]