insertionDiagram {gmoviz} | R Documentation

## Display number of copies of an insertion

### Description

Generates a diagram which displays insertions, showing their position, size and copy number. See `featureDiagram` for a more general function which can display other features of interest.

### Usage

    insertionDiagram(insertion_data, style = 1, either_side = "default",
      insertion_label = "default", sector_colours = nice_colours,
      sector_border_colours = nice_colours, start_degree = 180,
      custom_sector_width = NULL, coverage_rectangle = NULL,
      coverage_data = NULL, custom_ylim = NULL,
      space_between_sectors = 15, sector_labels = TRUE,
      sector_label_size = 1.3, sector_label_colour = "black",
      label_data = NULL, label_colour = "black", link_colour = "default",
      label_size = 1.1, xaxis = TRUE, xaxis_label_size = 0.9,
      xaxis_colour = "#747577", xaxis_spacing = 10,
      xaxis_spacing_unit = "deg", link_ends = "default",
      track_height = 0.15, internal = FALSE)

### Arguments

`insertion_data` | A `GRanges` or data frame describing the insertion. See below for the detailed format.
`style` | How the original sequence and insertions will be positioned around the circle. Choose from options 1, 2, 3 or 4. Please see the examples below or the vignette for what these options represent.
`either_side` | How much extra of the genome should be shown around the insertion site. Can be either a single number (e.g. `1000`, then 1000bp will be shown either side of the insertion site), a vector of length 2 (e.g. `c(2000, 13000)` in which case from 2000 to 13000 will be shown) or a GRanges (in which case all ranges in the GRanges object will be used to determine the start/end points of the sector)
`insertion_label` | The label(s) that will be applied to the insertions. If `'default'` then the name of the insertion will be used to label single copy insertions and a number will be used for multiple copy number insertions. Otherwise, `insertion_label` should be a vector with one element for each row of the insertion data, indicating the label that should be used for that insertion.
`sector_colours` | Either a single colour (which will be applied to all sectors) or a vector with the same length as the number of sectors/regions. This package includes 5 colour sets: `nice_colours`, `pastel_colours`, `bright_colours_transparent`, `bright_colours_opaque` and `rich_colours`. See `colourSets` for more information about these.
`sector_border_colours` | Same as `sector_colours`, only for the border of each sector.
`start_degree` | Where on the circle the first sector will start being drawn from (90 = 12 o'clock).
`custom_sector_width` | Normally, the size of each sector is proportional to its relative length, but `custom_sector_width` can change this. It is a vector of sector sizes (as proportions of the entire circle), given in the same order in which sectors are plotted: firstly 'chr1', 'chr2' ... through to 'chrX' and 'chrY' followed by any differently named sectors e.g. 'gene 1', plasmid' in alphabetical order.
`coverage_rectangle` | A vector containing the name(s) of any sector(s) that you would like to depict as 'coverage rectangles': filled in shapes that are a plot of the coverage data over that sector. See the example below or the vignette for an example of this.
`coverage_data` | A GRanges (or data frame) containing the coverage data to plot for those sectors in `coverage_rectangle`. To read this data in from a BAM file, please see the `getCoverage` function.
`custom_ylim` | A vector of length two containing the y (coverage) axis limits. No need to set if not using coverage rectangles or if you're happy with the default: c(0, maximum coverage).
`space_between_sectors` | Space between each sector.
`sector_labels` | If `TRUE`, labels ('chr1', 'chr2' etc.) will be drawn for each sector (recommended).
`sector_label_size` | Size of the sector labels.
`sector_label_colour` | Colour of the sector labels.
`label_data` | Data frame or GRanges containing the labels. If a GRanges, `label` should be a metadata column containing the character strings of the labels. `type` and `colour` can also be used to store additional information about the type (e.g. 'gene' or 'promoter') and colour of the label. This information can be used to colour code the labels by supplying the colour column as the `label_colour` parameter. Data frames should additionally include the `chr`, `start`, `end` which dictate the position of the label.
`label_colour` | Colour of the labels, can be either a single value (applied to all labels) or a vector with the same length as the number of labels (for colour-coding).
`link_colour` | The colour of the link: this should be a 6 digit hex code, the transparency is automatically added.
`label_size` | Size of the labels.
`xaxis` | If `TRUE`, an x (genomic position) xaxis will be plotted.
`xaxis_label_size` | Size of the x axis labels.
`xaxis_colour` | Colour of the x axis labels.
`xaxis_spacing` | Space between the x axis labels, in degrees. Alternatively, the string 'start_end' will place a label at the start and end of each sector only.
`xaxis_spacing_unit` | Either `"deg"` to draw ticks every certain number of degrees around the circle or `"bp"` to draw ticks every certain bp around the circle (be warned that when the scales for each sector are very different, it's best to use `"deg"`)
`link_ends` | How far the link extends in either direction. This is set automatically but if you want to edit it, provide a vector of length 2 with each element being between 0 (centre of circle) and 1 (right at the edge of the circle).
`track_height` | The height (vertical distance around the circle) that will be taken up by this track. Should be a number between 0 (none) and 1 (entire circle).
`internal` | For internal use only.

### Value

Generates an image displaying the copy number of the insertion(s) provided

### Insertion data format

The start, end and seqnames of insertion_data GRanges should describe the insertion site. Additionally, there are five metadata columns:

name

  A character string which will be used to label insertion. It is suggested to keep this label relatively short, if possible.

colour

  A character string of a colour to use. Supports hex colours (e.g. #000000) and named R colours (e.g. red).

shape

  The shape that will be used to represent the feature:

  - `'rectangle'` is a rectangle.

  - `'forward_arrow'` for a forwards facing arrow.

  - `'reverse_arrow'` for a backwards (reverse) facing arrow.

  It is suggested to use `'forward_arrow'`

length

  The length of the insertion

in_tandem

  The number of copies of the insert in tandem

The columns in_tandem, colour and shape are all optional. If you don't supply them, then default values will be added as follows:

in_tandem

  1 (only one copy inserted)

colour

  a colour allocated from `rich_colours`

shape

  `'forward_arrow'`

### Warning

If you choose to use a data frame to supply the insertion_data, please be careful to add the `stringsAsFactors=FALSE` argument. Otherwise, the colours may not be correct.

### See Also

`featureDiagram` for a more flexible function that takes a similar approach to representing features of interest.

### Examples

    ## one insertion with 4 tandem copies
    ## the data as a data.frame
    exampleins <- data.frame(
    chr='chr12', start=70905597, end=70917885, name='plasmid',
    colour='#7270ea', length=12000, in_tandem=11, shape='forward_arrow',
    stringsAsFactors=FALSE)

    ## or we can supply it as GRanges (same thing)
    exampleins <- GRanges(
    seqnames='chr12', ranges=IRanges(start=70905597, end=70917885),
    name='plasmid', colour='#7270ea', length=12000, in_tandem=11,
    shape='forward_arrow')

    ## plot it
    insertionDiagram(exampleins, either_side=c(70855503, 71398284))

    ## that was the default 'style'. The other 3 styles are:
    ## style 2
    insertionDiagram(exampleins, either_side=c(70855503, 71398284), style=2)

    ## style 3
    insertionDiagram(exampleins, either_side=c(70855503, 71398284), style=3)

    ## style 4
    insertionDiagram(exampleins, either_side=c(70855503, 71398284), style=4)

    ## 2 different insertions
    ## the data
    example2ins <- data.frame(
    chr=c('chr12', 'chr12'), start=c(70905597, 70705597),
    end=c(70917885, 70717885), name=c('plasmid1', 'plasmid2'),
    colour=c('#7270ea', '#ea7082'), length=c(12000, 10000),
    in_tandem=c(4, 8), shape=c('reverse_arrow', 'forward_arrow'),
    stringsAsFactors=FALSE)

    ## plot it
    insertionDiagram(example2ins, link_colour='#ffe677', start_degree=45)

[Package gmoviz version 1.0.1 Index]