make_homopolymer_plot: Make plot to compare accuracy per homopolymer length

In vladimirsouza/lrRNA-seq_benchmark: Figure out how to call varaints from Iso-Seq data

Make plot to compare accuracy per homopolymer length

Description

The function uses the output from function 'method_homopolymer_indels' to make a plot to compare how the accuracy vary according to the homopolymer length or not within homopolymers. Those accuracy measures can be either rates of TPs, FNs and FPs, or the precision, recall and F1-score.

Usage

make_homopolymer_plot(
  input_hom_table,
  variant_type,
  method_name,
  truth_name,
  hom_length_intervals,
  interval_names,
  to_calculate
)

Arguments

input_hom_table	A data.frame. The output of the function 'method_homopolymer_indels'.
variant_type	A 1-length string. The variant type. Possivle values are: "snp", "deletion", or "insertion".
method_name	A 1-length string. The name of the method to analyse.
truth_name	A 1-length string. The name of the ground-truth.
hom_length_intervals	A vector of integers. Must be the same length of 'interval_names'. The inferior limit for each interval for homopolymer length.
interval_names	A vector of strings. Must be the same length of 'hom_length_intervals'. The name of each interval of homopolymer length.
to_calculate	A 1-length string. Possible values are: "rates" or "pre_rec_f1".

Value

A list, in which the first element, named 'p', is a ggplot object, and the second element, named 'interval_counts', is a named vector of integers that stores the counts of variants in each interval specified by the x-axis of the plot in 'p'.

vladimirsouza/lrRNA-seq_benchmark documentation built on March 25, 2023, 9:29 p.m.