Plots the counts of unique haplotype IDs found in each reference range.
Usage
plotHaploCounts(object, ...)
# S4 method for class 'PHGDataSet'
plotHaploCounts(object, gr = NULL, geom = "l")
Arguments
- object
a
PHGDataSet
object- ...
Additional arguments, for use in specific methods
- gr
A
GRanges
object specifying a genomic range for filtering the haplotype data. IfNULL
, the function will plot the data across the entire dataset.- geom
A character string specifying the type of geometric representation for the plot. Accepted values are:
"l"
for lines (default),"b"
for bars,"p"
for points.
If an invalid value is provided, the function will raise an error.
Value
A ggplot
object visualizing the haplotype counts. When
gr
is NULL
, the plot shows the number of unique haplotypes
across reference positions. When gr
is provided, the plot is filtered
to display haplotype counts within the specified range.
Details
When no genomic range is provided (i.e., gr = NULL
), the function
plots the number of unique haplotypes across the entire reference genome or
dataset. This will default to point geometry regardless of the value
provided within the geom
parameter. If a genomic range is provided,
it filters the data based on overlaps between the reference ranges in the
dataset and the query range. In both cases, the resulting plot uses
ggplot2
for visualization, and different geometries can be selected
via the geom
parameter.