gmovizInitialise: Initialise the layout of the circular plot

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

Description

Draws the ideogram (sectors around a circle representing sequences of interest, like chromosomes), labels and genomic axis in preparation for the addition of other tracks like drawFeatureTrack or drawLinegraphTrack.

Usage

gmovizInitialise(ideogram_data, start_degree = 90,
  space_between_sectors = 1, zoom_sectors = NULL, zoom_size = 0.055,
  remove_unzoomed = TRUE, zoom_prefix = "zoomed_",
  custom_sector_width = NULL, track_height = 0.1,
  sector_colours = nice_colours, sector_border_colours = nice_colours,
  coverage_rectangle = NULL, coverage_data = NULL,
  custom_ylim = NULL, sector_labels = TRUE, sector_label_size = 0.9,
  sector_label_colour = "black", xaxis = TRUE,
  xaxis_orientation = "top", xaxis_label_size = 0.75,
  xaxis_colour = "#747577", xaxis_spacing = 10,
  xaxis_spacing_unit = "deg", label_data = NULL,
  label_colour = "black", label_size = 0.85,
  space_between_labels = 0.4, label_orientation = "outside",
  sort_sectors = TRUE)

Arguments

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.
start_degree	Where on the circle the first sector will start being drawn from (90 = 12 o'clock).
space_between_sectors	Space between each sector.
zoom_sectors	A character vector of sectors that should be 'zoomed' (made bigger than usual, useful to show shorter sequences like plasmids alongside longer sequences like chromosomes).
zoom_size	The size of the zoomed chromosome, as a proportion of the entire circle (0 = invisible, 1 = entire circle filled). The default value of 0.055 is good for displaying something small (e.g. plasmid) alongside something large (e.g. chromosomes).
remove_unzoomed	If TRUE, the sectors in zoom_sectors will only appear in their zoomed form. If FALSE, both the zoomed and unzoomed versions will be plotted.
zoom_prefix	A character prefix that will be applied to zoomed sequences to distinguish them from non-zoomed ones.
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.
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).
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.
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).
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.
xaxis	If TRUE, an x (genomic position) xaxis will be plotted.
xaxis_orientation	Either 'top' to put the x axis on the outside of the circle or 'bottom' to put it on the inside.
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")
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.
space_between_labels	Space between the labels
label_orientation	'outside' to put the labels on the outside of the circle, 'inside' to put them on the inside.
sort_sectors	If TRUE, the sectors will be plotted around the circle in alphabetical order. Otherwise, they will be in the order in which they appear in ideogram_data

Value

Generates an image of the initial ideogram track which can then be added to with various other functions.

See Also

The drawScatterplotTrack, drawFeatureTrack and drawLinegraphTrack, which can be used to add information to this plot. Also getIdeogramData which can be used to read in the needed ideogram data for this function.

Examples

## normal/standard usage
ideogram <- data.frame(chr=paste0('chr', c(1:19, 'X', 'Y')),
start=rep(0, 21),
end=c(195471971, 182113224, 160039680, 156508116, 151834684, 149736546,
145441459, 129401213, 124595110, 130694993, 122082543, 120129022,
120421639, 124902244, 104043685, 98207768, 94987271, 90702639, 61431566,
171031299, 91744698))
gmovizInitialise(ideogram)

## zooming a sector
gmovizInitialise(ideogram, zoom_sectors='chr19', zoom_size=0.2)

## custom sector width
small_ideogram <- data.frame(chr=c('region 1', 'region 2', 'region 3'),
start=c(0, 0, 0), end=c(10000, 12000, 10000))
gmovizInitialise(small_ideogram, custom_sector_width=c(0.3, 0.3, 0.3))

## coverage rectangle
path <- system.file('extdata', 'ex1.bam', package='Rsamtools')
ideo <- getIdeogramData(path, wanted_chr='seq1')
coverage <- getCoverage(bam_file=path, regions_of_interest='seq1',
window_size=30)
gmovizInitialise(ideo, coverage_rectangle='seq1', coverage_data=coverage)

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