Last data update: 2014.03.03

 R: Alignment geoms for GRanges object
geom_alignmentR Documentation

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",
                          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, or a list of, filter object(s) extending BasicFilter-class.

cds.rect.h

cds heights.

exon.rect.h

exon heights.

utr.rect.h

utr heights.

label.color

label color.

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")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ggbio)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: ggplot2
Need specific help about ggbio? try mailing 
 the maintainer or visit http://tengfei.github.com/ggbio/

Attaching package: 'ggbio'

The following objects are masked from 'package:ggplot2':

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim

Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ggbio/geom_alignment-method.Rd_%03d_medium.png", width=480, height=480)
> ### Name: geom_alignment
> ### Title: Alignment geoms for GRanges object
> ### Aliases: geom_alignment geom_alignment,GRanges-method
> ###   geom_alignment,GRangesList-method geom_alignment,OrganismDb-method
> ###   geom_alignment,missing-method geom_alignment,uneval-method
> ###   geom_alignment,TxDbOREnsDb-method geom_alignment,BamFile-method
> 
> ### ** Examples
> 
> set.seed(1)
> N <- 100
> require(GenomicRanges)
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
> ## ======================================================================
> ##  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))
Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.
Scale for 'fill' is already present. Adding another scale for 'fill', which
will replace the existing scale.
> 
> ## ======================================================================
> ##  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)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> 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"])
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
"gap" not in any of the valid gene feature terms "cds", "exon", "utr"
Constructing graphics...
> p1 <- ggplot(txdb) + geom_alignment(which = genesymbol["RBM17"])
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
"gap" not in any of the valid gene feature terms "cds", "exon", "utr"
Constructing graphics...
> p1
> p2 <- ggplot(txdb) + geom_alignment(which = genesymbol["RBM17"], stat = "reduce")
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
"gap" not in any of the valid gene feature terms "cds", "exon", "utr"
Constructing graphics...
reduce alignemnts...
> 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")
Parsing transcripts...
Parsing exons...
Parsing cds...
Parsing utrs...
------exons...
------cdss...
------introns...
------utr...
aggregating...
Done
"gap" not in any of the valid gene feature terms "cds", "exon", "utr"
Constructing graphics...
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO