plotValleyDistance {cfDNAPro} | R Documentation

## Plot the inter-valley distance of fragment size distance distribution

### Description

Plot the inter-valley distance of fragment size distance distribution

### Usage

    plotValleyDistance(x, order, type, mincount, xlim, ...)

### Arguments

`x` | A long-format dataframe contains the inter-valley distance, a template please refer to the result of 'callValleyDistance' function.
`order` | The groups show in the final plot, the input value should be vector, e.g. ‘groups=c(’group1','group2')', default is all folders in the folder path.
`type` | The plot type, default is line plot, now only support line plot. Don't change this parameter in this version, keep it as default.
`mincount` | Minimum count value of inter valley distance, count number less than this value will be removed first, then proportion of each count value will be calculated. Default value is 0.
`xlim` | The x axis range shown in the plot. Default is c(8,13).
`...` | Further arguments passed to or from other methods.

### Value

The function returns the line plot of inter valley distance.

### Author(s)

Haichao Wang

### Examples

    # Get the path to example data.
    path <- examplePath("groups_picard")

    # Calculate the inter-valley distance.
    df <- callValleyDistance(path = path)

    # Plot the inter-valley distance.
    plot <- plotValleyDistance(df,
        xlim = c(8, 13),
        mincount = 2
    )

[Package cfDNAPro version 1.0.0 Index]