plot_mismatches: Plots mismatches using ggplot2.

In valenlab/amplican: Automated analysis of CRISPR experiments

Plots mismatches using ggplot2.

Description

Plots mismatches in relation to the amplicon, assumes your reads are relative to the respective amplicon sequences predicted cut sites. Top plot is for the forward reads, middle one shows amplicon sequence, and bottom plot is for reverse reads.

Usage

plot_mismatches(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. They have to have the same amplicon, amplicons on the reverse strand will be reverse complemented to match forward strand amplicons.
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

(mismatches plot) gtable object of mismatches plot

See Also

Other specialized plots: metaplot_deletions(), metaplot_insertions(), metaplot_mismatches(), plot_cuts(), plot_deletions(), plot_heterogeneity(), plot_insertions(), 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)
id <- c('ID_1', 'ID_3'); cut_buffer = 5; xlab_spacing = 4;
p <- plot_mismatches(alignments, config, c('ID_1', 'ID_3'))
ggplot2::ggsave("~/test.png", p, width = 25, units = "in")

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