plotSingleGroup: Plot the raw fragment size metrics of single group in a...

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

Plot the raw fragment size metrics of single group in a single plot, colored by samples.

Description

Plot the raw fragment size metrics of single group in a single plot, colored by samples.

Usage

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

Arguments

x	A long-format dataframe contains the metrics of different cohort.
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(0,0.035)'.
vline	Vertical dashed lines, default value is 'c(81,167)'.
order	The groups show in the final plot, the input value should be vector, e.g. ‘order = c(’group1')“, default is all groups/cohorts in the folder path.
plot	The plot type, default is 'all' which means both proportion, cdf and 1-cdf plots will be shown.
...	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 the only the group specified..
plot <- plotSingleGroup(x = df, order = c("cohort_1"))

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