transform: Transform GRanges to different coordinates and layout

In lawremi/biovizBase: Basic graphic utilities for visualization of genomic data.

Description

Used for coordiante genome transformation, other transformation in circular view.

Usage

## S4 method for signature 'GRanges'
transformToGenome(data, space.skip = 0.1, chr.weight
= NULL)
## S4 method for signature 'GRangesList'
transformToGenome(data, space.skip = 0.1,
chr.weight = NULL)

## S4 method for signature 'GRanges'
transformToArch(data, width = 1)
transformToCircle(data, x = NULL, y = NULL, ylim = NULL, 
                  radius = 10, trackWidth =10,
                  direction = c("clockwise", "anticlockwise"),
                   mul = 0.05)


transformToRectInCircle(data, y = NULL, space.skip = 0.1, trackWidth = 10, radius = 10,
                      direction = c("clockwise", "anticlockwise"),
                      n = 100, mul = 0.05, chr.weight = NULL)

transformToBarInCircle(data, y = NULL, space.skip = 0.1, trackWidth = 10, radius = 10,
                     direction = c("clockwise", "anticlockwise"),
                      n = 100, mul = 0.05, chr.weight = NULL)

transformToSegInCircle(data, y = NULL, space.skip = 0.1, trackWidth = 10, radius = 10,
                      direction = c("clockwise", "anticlockwise"), n =
                      100, chr.weight = NULL)


transformToLinkInCircle(data, linked.to, space.skip = 0.1, trackWidth = 10, radius = 10,
                      link.fun = function(x, y, n = 100) bezier(x, y, evaluation = n),
                      direction = c("clockwise", "anticlockwise"), chr.weight = NULL)

transformDfToGr(data, seqnames = NULL, start = NULL, end = NULL,
                            width = NULL, strand = NULL,
                            to.seqnames = NULL, to.start = NULL, to.end = NULL,
                            to.width = NULL, to.strand = NULL, linked.to
                            = to.gr)



## S4 method for signature 'GRanges'
transformToDf(data)

is_coord_genome(data)

Arguments

data	a GRanges object. for function transformDfToGr it's data.frame.
x	character for variable as x axis used for transformation.
y	character for variable as y axis used for transformation.
ylim	numeric range to control the ylimits on tracks when 'y' information is involved.
space.skip	numeric values indicates skipped ratio of whole space, not skipped space is identical between each space.
radius	numeric value, indicates radius when transform to a circle.
trackWidth	numeric value, for track width.
direction	"clockwise" or "counterclockwise", for layout or transform direction to circle.
mul	numeric value, passed to expand_range function, to control margin of y in the track.
n	integer value, control interpolated points numbers.
linked.to	a column name of GRanges object, indicate the linked line's end point which represented as a GRanges too..
link.fun	function used to generate linking lines.
seqnames	character or integer values for column name or index indicate variable mapped to seqnames, default NULL use "seqnames".
start	character or integer values for column name or index indicate variable mapped to start, default NULL use "start".
end	character or integer values for column name or index indicate variable mapped to end, default NULL use "end".
width	character or integer values for column name or index indicate variable mapped to width, default NULL use "width".
strand	character or integer values for column name or index indicate variable mapped to strand, default NULL use "strand".
to.seqnames	character or integer values for column name or index indicate variable mapped to linked seqnames, default NULL, create GRanges without new GRanges attached as column. If this varialbe is not NULL, this mean you try to parse linked GRanges object.
to.start	character or integer values for column name or index indicate variable mapped to start of linked GRanges, default NULL use "to.start".
to.end	character or integer values for column name or index indicate variable mapped to end of linked GRanges, default NULL use "to.end".
to.width	character or integer values for column name or index indicate variable mapped to width of linked GRanges, default NULL use "to.width".
to.strand	character or integer values for column name or index indicate variable mapped to strand, default NULL use "to.strand" or just use *.
chr.weight	numeric vectors which sum to <1, the names of vectors has to be matched with seqnames in seqinfo, and you can only specify part of the seqnames, other lengths of chromosomes will be assined proportionally to their seqlengths, for example, you could specify chr1 to be 0.5, so the chr1 will take half of the space and other chromosomes squeezed to take left of the space.

Value

A GRanges object, with calculated new variables, including ".circle.x" for transformed x position, ".circle.y" for transformed y position, ".circle.angle" for transformed angle.

Author(s)

Tengfei Yin

Examples

library(biovizBase)
library(GenomicRanges)
set.seed(1)
gr1 <- GRanges("chr1", IRanges(start = as.integer(runif(20, 1, 2e9)),
width = 5))
gr2 <- GRanges("chr2", IRanges(start = as.integer(runif(20, 1, 2e9)),
width = 5))
gr <- c(gr1, gr2)
gr.t <- transformToGenome(gr, space.skip = 0.1)
is_coord_genome(gr.t)
transformToCircle(gr.t)
transformToRectInCircle(gr)
transformToSegInCircle(gr)
values(gr1)$to.gr <- gr2
transformToLinkInCircle(gr1, linked.to = "to.gr")

lawremi/biovizBase documentation built on Dec. 21, 2021, 9:42 a.m.