plot_variants {amplican} | R Documentation

## Plots most frequent variants using ggplot2.

### Description

This function plots variants in relation to the amplicon. Shows sequences of top mutants without aggregating on deletions, insertions and mismatches.

### Usage

    plot_variants(alignments, config, id, cut_buffer = 5, top = 10,
      annot = "codon", summary_plot = TRUE)

### 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.
`top` | (numeric) Specify number of most frequent reads to plot. By default it is 10. Check `plot_heterogeneity` to see how many reads will be enough to give good overview of your variants.
`annot` | ("codon" or NA) What to display for annotation top plot. When NA will not display anything, also not display total summary.
`summary_plot` | (boolean) Whether small summary plot in the upper right corner should be displayed. Top bar summarizes total reads with frameshift (F), reads with InDels without Frameshift (InDel) and reads without InDels (Match). Bottom bar summarizes percentage and how InDels are distributed towards Insertions (Ins), Deletions (Del) and Mixed Insertions/Deletions (InDel).
    annot            on    | off

### Details

Top plot shows all six possible frames for given amplicon. Amino acids are colored as follows:

Small nonpolar | G, A, S, T | Orange
Hydrophobic | C, V, I, L, P, F, Y, M, W | Green
Polar | N, Q, H | Magenta
Negatively charged | D, E | Red
Positively charged | K, R | Blue
Other | eg. *, U, + | Grey

Variant plot shows amplicon reference, UPPER letters which were the basis for window selection are highlighted with dashed white box (guideRNA). Black triangles are reflecting insertion points. Dashed letters indicate deletions. Table associated with variant plot represents:

- Freq - Frequency of given read in experiment. Variants are ordered by frequency value.

- Count - Represents raw count of this variant reads in experiment.

- F - Sum of deletion and insertion widths of events overlapping presented window. Green background indicates frameshift.

### Value

(variant plot) gtable object of variants plot

### Note

This function is inspired by `plotAlignments`.

### See Also

Other specialized plots: `metaplot_deletions`, `metaplot_insertions`, `metaplot_mismatches`, `plot_cuts`, `plot_deletions`, `plot_heterogeneity`, `plot_insertions`, `plot_mismatches`

### 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_variants(alignments[alignments$consensus & alignments$overlaps, ],
                       config, c('ID_1','ID_3'))

[Package amplican version 1.2.1 Index]