plotPeakDistance: Plot the inter-peak distance of fragment size distance...

In hw538/cfDNAPro: cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA

Plot the inter-peak distance of fragment size distance distribution

Description

Plot the inter-peak distance of fragment size distance distribution

Usage

plotPeakDistance(x, summarized, order, type, mincount, xlim, ...)

Arguments

x	A long-format dataframe contains the inter-peak distance, a template please refer to the result of 'callPeakDistance' function.
summarized	Logical value, describe whether the x is summarzied already. summarized means the count and proportion of each interpeak_dist.
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 peak 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 peak distance.

Author(s)

Haichao Wang

Examples

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

# Calculate the inter-peak distance.
df <- callPeakDistance(path = path)

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

hw538/cfDNAPro documentation built on Aug. 13, 2024, 2:58 p.m.