plotMode: Plot mode fragment size

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

Plot mode fragment size

Description

Plot mode fragment size

Usage

plotMode(x, order, type, mincount, hline, ...)

Arguments

x	A long-format dataframe contains the interpeak distance, a template please refer to the result of "callPeakdist" 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, could choose "bin" or "stacked" chart. Default is bin plot.
mincount	Minimum count of mode fragment size that will be included. Count number smaller than this value will be removed first, then proportion of each count value will be calculated. Default value is 0.
hline	The horizontal lines added to the bin plot. Default lines will be 'c(81,112,170)'.
...	Further arguments passed to or from other methods.

Value

The function returns the plot.

Author(s)

Haichao Wang

Examples

# Get the path to example data.
path <- examplePath("groups_picard")
# Calculate the modes.
df <- callMode(path = path)
# Plot modes.
plot <- plotMode(df, hline = c(80, 111, 170))

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