plot_deletions {amplican} | R Documentation

## Plots deletions using ggplot2.

### Description

This function plots deletions in relation to the amplicon, assumes events are relative to the expected cut site. Top plot is for the forward reads, middle one shows amplicon sequence, and bottom plot is for reverse reads.

### Usage

    plot_deletions(alignments, config, id, cut_buffer = 5,
      xlab_spacing = 4, over = "overlaps")

### Arguments

`alignments` | (data.frame) Loaded alignment information from alignments.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.
`over` | (string) Specify which columns contains overlaps with expected cut sites generated by `amplicanOverlap`

### Value

(deletions plot) gtable object of deletions plot

### See Also

Other specialized plots: `metaplot_deletions`, `metaplot_insertions`, `metaplot_mismatches`, `plot_cuts`, `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)
    p <- plot_deletions(alignments[alignments$consensus, ],
                        config, c('ID_1','ID_3'))

[Package amplican version 1.8.2 Index]