geom_alignment-method: Alignment geoms for GRanges object

In tengfei/ggbio: Visualization tools for genomic data

Alignment geoms for GRanges object

Description

Show interval data as alignment.

Usage

## S4 method for signature 'GRanges'
geom_alignment(data, ..., xlab, ylab, main, facets = NULL, stat =
                 c("stepping", "identity"), range.geom = c("rect",
                 "arrowrect"), gap.geom = c("chevron", "arrow",
                 "segment"), rect.height = NULL, group.selfish = TRUE,
                  label = TRUE)

## S4 method for signature 'TxDbOREnsDb'
geom_alignment(data, ..., which, columns = c("tx_id", "tx_name",
                 "gene_id"), names.expr = "tx_name", facets = NULL,
                 truncate.gaps = FALSE, truncate.fun = NULL, ratio =
                 0.0025)

## S4 method for signature 'GRangesList'
geom_alignment(data, ..., which = NULL,
                          cds.rect.h = 0.25,
                          exon.rect.h = cds.rect.h,
                          utr.rect.h = cds.rect.h/2,
                          xlab, ylab, main,
                          facets = NULL, geom = "alignment",
                          stat = c("identity", "reduce"),
                          range.geom = "rect",
                          gap.geom = "arrow",
                          utr.geom = "rect",
                          names.expr = NULL,
                          label = TRUE,
                          label.color = "gray40",
                          label.size = 3,
                          arrow.rate = 0.015,
                          length = unit(0.1, "cm"))

## S4 method for signature 'OrganismDb'
geom_alignment(data, ..., which,
                   columns = c("TXNAME", "SYMBOL", "TXID", "GENEID"),
                   names.expr = "SYMBOL",
                   facets = NULL,
                   truncate.gaps = FALSE,
                   truncate.fun = NULL, ratio = 0.0025
                   )

Arguments

data	A GRanges, data.frame, TxDb or EnsDb object.
...	Extra parameters such as aes() passed.
which	GRanges object to subset the TxDb or EnsDb object. For EnsDb: can also be a single object extending AnnotationFilter, an AnnotationFilterList combining such objects or a filter expression in form of a formula.
cds.rect.h	cds heights.
exon.rect.h	exon heights.
utr.rect.h	utr heights.
label.color	label color.
label.size	label size.
arrow.rate	arrow rate.
length	arrow length.
columns	columns to get from object.
xlab	Label for x
ylab	Label for y
main	Title for plot.
facets	Faceting formula to use.
stat	For GRanges: Character vector specifying statistics to use. "stepping" with randomly assigned stepping levels as y varialbe. "identity" allow users to specify y value in aes. For TxDb: defualt "identity" give full gene model and "reduce" for reduced model.
gap.geom	Geom for 'gap' computed from the data you passed based on the group information.
rect.height	Half height of the arrow body.
group.selfish	Passed to addStepping, control whether to show each group as unique level or not. If set to FALSE, if two groups are not overlapped with each other, they will probably be layout in the same level to save space.
truncate.gaps	logical value indicate to truncate gaps or not.
truncate.fun	shrinkage function. Please see shrinkagefun in package biovizBase.
ratio	used in maxGap.
geom	geometric object. only support "gene" now.
range.geom	geom for main intevals or exons.
utr.geom	geom for utr region.
names.expr	expression for showing y label.
label	logical value. Whether to label the intervals with names specified by argument names.expr.

Value

A 'Layer'.

Author(s)

Tengfei Yin

Examples

set.seed(1)
N <- 100
require(GenomicRanges)
## ======================================================================
##  simmulated GRanges
## ======================================================================
gr <- GRanges(seqnames =
              sample(c("chr1", "chr2", "chr3"),
                     size = N, replace = TRUE),
              IRanges(
                      start = sample(1:300, size = N, replace = TRUE),
                      width = sample(70:75, size = N,replace = TRUE)),
              strand = sample(c("+", "-", "*"), size = N,
                replace = TRUE),
              value = rnorm(N, 10, 3), score = rnorm(N, 100, 30),
              sample = sample(c("Normal", "Tumor"),
                size = N, replace = TRUE),
              pair = sample(letters, size = N,
                replace = TRUE))


## ======================================================================
##  default
## ======================================================================
ggplot(gr) + geom_alignment()
## or
ggplot() + geom_alignment(gr)

## ======================================================================
##  facetting and aesthetics
## ======================================================================
ggplot(gr) + geom_alignment(facets = sample ~ seqnames, aes(color = strand, fill = strand))

## ======================================================================
##  stat:stepping
## ======================================================================
ggplot(gr) + geom_alignment(stat = "stepping", aes(group = pair))

## ======================================================================
##  group.selfish controls when
## ======================================================================
ggplot(gr) + geom_alignment(stat = "stepping", aes(group = pair), group.selfish = FALSE)

## =======================================
##  main/gap geom
## =======================================
ggplot(gr) + geom_alignment(range.geom = "arrowrect", gap.geom = "chevron")

## =======================================
##  For TxDb
## =======================================
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
data(genesymbol, package = "biovizBase")
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
## made a track comparing full/reduce stat.
ggbio() + geom_alignment(data = txdb, which = genesymbol["RBM17"])
p1 <- ggplot(txdb) + geom_alignment(which = genesymbol["RBM17"])
p1
p2 <- ggplot(txdb) + geom_alignment(which = genesymbol["RBM17"], stat = "reduce")
tracks(full = p1, reduce = p2, heights = c(3, 1))
tracks(full = p1, reduce = p2, heights = c(3, 1)) + theme_tracks_sunset()
tracks(full = p1, reduce = p2, heights = c(3, 1)) +
     theme_tracks_sunset(axis.line.color = NA)
## change y labels
ggplot(txdb) + geom_alignment(which = genesymbol["RBM17"], names.expr = "tx_id:::gene_id")

tengfei/ggbio documentation built on Nov. 5, 2023, 6:17 a.m.