plotAllToOne: Plot the raw fragment size metrics (e.g. proportion, cdf and...

In cfDNAPro: This Package Helps Characterise and Visualise Whole Genome Sequencing Data from Liquid Biopsy

Description

Plot the raw fragment size metrics (e.g. proportion, cdf and 1-cdf) of all groups with different colors in a single plot

Usage

plotAllToOne(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' which means all of proportion, cdf and 1-cdf plots will be shown.
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(0,0.035)'.
...	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 sizes.
df <- callSize(path = path)
# Plot all samples from multiple groups into one figure.
plot <- plotAllToOne(df)

cfDNAPro documentation built on Nov. 8, 2020, 6:49 p.m.