transform: Transform GRanges to different coordinates and layout

Description Usage Arguments Value Author(s) Examples

Description

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

Usage

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## 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

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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")

Bioconductor-mirror/biovizBase documentation built on June 1, 2017, 5:21 a.m.