multipleInsertionDiagram {gmoviz} | R Documentation

## Display multiple insertion events around a genome

### Description

Generates a diagram which displays multiple insertion events (as displayed using the `insertionDiagram` function) around a central genome

### Usage

    multipleInsertionDiagram(insertion_data, genome_ideogram_data,
      either_side = "default", track_height = 0.15, style = 1,
      colour_set = nice_colours, coverage_rectangle = NULL,
      coverage_data = NULL, label_data = NULL, label_colour = "black",
      label_size = 1, xaxis_spacing = "start_end")

### Arguments

`insertion_data` | A `GRanges` or data frame describing each of the insertion events. Please see `insertionDiagram` for a detailed description of the format.
`genome_ideogram_data` | Either a `GRanges` representing regions of interest or a data frame in bed format (containing the chr, start and end columns). If you want to read in data from file, please see the `getIdeogramData` function.
`either_side` | How much extra of the genome should be shown around the insertion site. See `insertionDiagram` for a description of the different ways you can specify `either_side`, but note that for this function you need to supply either one value (which will apply to all of the events) or a named list of values (with one element per event. The names should be the names of the insertion _NOT_ the names of the chromosomes).
`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) that will apply to all of the events.
`style` | How the original sequence and insertions are positioned around the circle (style 1, 2, 3 or 4). Please see the examples of the `insertionDiagram` function or the vignette for what each of these options look like. This should be either a single value (which will apply to all of the events) or a named vector of values (with one element per event).
`colour_set` | The set of colours that will be used to create the diagram. For simplicity, it isn't possible to specify precisely the colour of each sector and link in the diagram (but you can easily edit them by saving the diagram in a vectorised format and opening it in any vector graphics editing program). See `colourSets` for the built-in gmoviz colour sets or make your own (should be a vector of hex colours; must have a length greater than or equal to the number of rows of genome_ideogram_data)
`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.
`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).
`label_size` | Size of the 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. Accepts only a single value which will be applied to all events.

### Value

Generates an image of the multiple insertion events provided.

### Warning

Due to space limitations, it isn't possible to display more than 8 events or more than 3 events in the same quarter of the circle. If you have more events than this, please consider splitting them across two or more figures.

### See Also

`insertionDiagram` for a function which generates the figures for each of the individual events and `gmovizInitialise` for the function which draws the central genome

### Examples

    ## the data
    ideogram_data <- GRanges(
    seqnames=paste0('chr', 1:6), ranges=IRanges(start=rep(0, 6),
     end=rep(12000, 6)))
    insertion_data <- GRanges(
    seqnames = c('chr1', 'chr5'),
    ranges = IRanges(start = c(4000, 2000), end = c(4100, 2200)),
    name = c('ins1', 'ins5'), length = c(100, 200))

    ## the plot
    multipleInsertionDiagram(insertion_data=insertion_data,
                             genome_ideogram_data=ideogram_data)
    ## with coverage and labels
    example_labels <- GRanges(seqnames=c('chr1', 'chr5'),
                              ranges=IRanges(start=c(4000, 2000),
                              end=c(4120, 2200)),
                              label=c('Gene A', 'Gene B'),
                              colour=c('red', 'blue'))

    example_coverage <- GRanges(
    seqnames = c(rep('chr1', 100), rep('chr5', 100)),
    ranges = IRanges(start=c(seq(4000, 4099, length.out=100),
                             seq(2000, 2199, length.out=100)),
                     end=c(seq(4001, 4100, length.out=100),
                           seq(2001, 2200, length.out=100))),
                     coverage=c(runif(100, 0, 25), runif(100, 0, 15)))
    multipleInsertionDiagram(insertion_data=insertion_data,
                             genome_ideogram_data=ideogram_data,
                             label_data=example_labels,
                             label_colour=example_labels$colour,
                             coverage_rectangle=c('chr1', 'chr5'),
                             coverage_data=example_coverage)
    ## changing either_side and style
    either_side_GRange <- GRanges('chr5', IRanges(1000, 3200))
    multipleInsertionDiagram(insertion_data=insertion_data,
                             genome_ideogram_data=ideogram_data,
                             style=c('ins1'=1, 'ins5'=4),
                             either_side=list('ins1'=500,
                                                'ins5'=either_side_GRange))

[Package gmoviz version 1.4.0 Index]