metaplot_deletions: MetaPlots deletions using ggplot2.

In valenlab/amplican: Automated analysis of CRISPR experiments

MetaPlots deletions using ggplot2.

Description

This function plots deletions in relation to the amplicons for given selection vector that groups values by given config group. All reads should already be converted to their relative position to their respective amplicon using amplicanMap. Top plot is for the forward reads and bottom plot is for reverse reads.

Usage

metaplot_deletions(alnmt, config, group, selection, over = "overlaps")

Arguments

alnmt	(data.frame) Loaded alignment information from events_filtered_shifted_normalized.csv file.
config	(data.frame) Loaded table from config_summary.csv file.
group	(string) Name of the column from the config file to use for grouping. Events are subselected based on this column and values from selection.
selection	(string or vector of strings) Values from config column specified in group argument.
over	(string) Specify which column contains overlaps with expected cut sites generated by amplicanOverlap

Value

(deletions metaplot) ggplot2 object of deletions metaplot

See Also

Other specialized plots: metaplot_insertions(), metaplot_mismatches(), plot_cuts(), 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)
metaplot_deletions(alignments[alignments$consensus, ],
                   config, "Group", "Betty")

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