insertionDiagram: Display number of copies of an insertion

In gmoviz: Seamless visualization of complex genomic variations in GMOs and edited cell lines

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)

gmoviz documentation built on Nov. 8, 2020, 5:41 p.m.