plotMetrics {cfDNAPro} | R Documentation

## Plot the fragment size metrics (i.e. proportion, cdf and 1-cdf)

### Description

Plot the fragment size metrics (i.e. proportion, cdf and 1-cdf)

### Usage

    plotMetrics(x, order, plot, vline, xlim, ylim, ...)

### Arguments

`x` | A long-format dataframe contains the metrics of different cohort.
`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
`plot` | The plot type, default is 'all': both median and mean metrics will be shown. They will include: mean_prop, mean_cdf, mean_1-cdf, median_prop, median_cdf, median_1-cdf. Could also specify as "median" or "mean".
`vline` | Vertical dashed lines, default value is c(81,167).
`xlim` | The x axis range shown in the plot. Default is c(0,500).
`ylim` | The y axis range shown in the fraction of fragment size plots. Default is c(0,0.0125).
`...` | Further arguments passed to or from other methods.

### Value

The function returns a list plots.

### Author(s)

Haichao Wang

### Examples

    # Get the path to example data.
    path <- examplePath("groups_picard")
    # Calculate the metrics.
    df <- callMetrics(path = path)
    # Plot metrics.
    plot <- plotMetrics(df,
        plot = "median",
        order = c("cohort_1", "cohort_2")
    )

[Package cfDNAPro version 1.0.0 Index]