plot_cuts: Plots cuts using ggplot2.

In valenlab/amplican: Automated analysis of CRISPR experiments

Plots cuts using ggplot2.

Description

This function plots cuts in relation to the amplicon with distinction for each ID.

Usage

plot_cuts(alignments, config, id, cut_buffer = 5, xlab_spacing = 4)

Arguments

alignments	(data.frame) Loaded alignment information from alignments_events.csv file.
config	(data.frame) Loaded table from config_summary.csv file.
id	(string or vector of strings) Name of the ID column from config file or name of multiple IDs if it is possible to group them. First amplicon will be used as the basis for plot.
cut_buffer	(numeric) Default is 5, you should specify the same as used in the analysis.
xlab_spacing	(numeric) Spacing of the x axis labels. Default is 4.

Value

(cuts plot) gtable object of cuts plot

See Also

Other specialized plots: metaplot_deletions(), metaplot_insertions(), metaplot_mismatches(), plot_deletions(), plot_heterogeneity(), plot_insertions(), plot_mismatches(), plot_variants()

Examples

#example config
config <- read.csv(system.file("extdata", "results", "config_summary.csv",
                               package = "amplican"))
#example alignments results
alignments_file <- system.file("extdata", "results", "alignments",
                               "events_filtered_shifted_normalized.csv",
                               package = "amplican")
alignments <- read.csv(alignments_file)
plot_cuts(alignments[alignments$consensus & alignments$overlaps, ],
          config, c('ID_1','ID_3'))

valenlab/amplican documentation built on Jan. 28, 2024, 5:10 a.m.