Gviz

1) Introduction

为了理解基因组数据，通常旨在在基因组浏览器中绘制这样的数据，以及各种基因组注释特征，例如基因或转录物模型，CpG岛，重复区域等。这些功能可以从ENSEMBL或UCSC等公共数据库中提取，也可以在内部生成或策划。许多当前可用的基因组浏览器在显示基因组注释数据方面做了合理的工作，并且存在从R内部连接到其中一些的选项（例如，使用rtracklayer包）。然而，这些解决方案都没有提供完整的Rgraphics系统以多种不同方式显示大数值数据的灵活性。 Gviz软件包旨在通过提供结构化可视化框架来绘制基因组坐标上的任何类型的数据来缩小这一差距。它松散地基于GenomeGraphs包，但为了提高性能和灵活性，重新构建了完整的类层次结构以及所有绘图方法，所有绘图都是使用网格图形系统完成的，并且几个专门的注释类允许集成来自UCSC或ENSEMBL等来源的公开可用的基因组注释数据。

2）Basic Features

if("Gviz" %in% rownames(installed.packages()) == FALSE) {source("http://bioconductor.org/biocLite.R");biocLite("Gviz")}

suppressMessages(library(Gviz))

ls('package:Gviz')

library(GenomicRanges)

data(cpgIslands)     #以GC岛数据集为例

class(cpgIslands)

chr <- as.character(unique(seqnames(cpgIslands)))

gen <- genome(cpgIslands)

atrack <- AnnotationTrack(cpgIslands, name = "CpG")

plotTracks(atrack)

gtrack <- GenomeAxisTrack()

plotTracks(list(gtrack, atrack))

itrack <- IdeogramTrack(genome = gen, chromosome = chr)

plotTracks(list(itrack, gtrack, atrack))

由基本特征可以知道，GVIZ和ggplot2 好像 道理是一样的，一层累积一层添加元素。我们再以下面数据集为例：

data(geneModels)

grtrack <- GeneRegionTrack(geneModels, genome = gen,chromosome = chr, name = "Gene Model")

plotTracks(list(itrack, gtrack, atrack, grtrack))

plotTracks(list(itrack, gtrack, atrack, grtrack),from = 26700000, to = 26750000)

plotTracks(list(itrack, gtrack, atrack, grtrack),extend.left = 0.5, extend.right = 1e+06)

plotTracks(list(itrack, gtrack, atrack, grtrack),

           extend.left = 0.5, extend.right = 1e+06, col = NULL)

library(BSgenome.Hsapiens.UCSC.hg19)

strack <- SequenceTrack(Hsapiens, chromosome = chr)

plotTracks(list(itrack, gtrack, atrack, grtrack,

                strack), from = 26591822, to = 26591852, cex = 0.8)

set.seed(255)

lim <- c(26700000, 26750000)

coords <- sort(c(lim[1], sample(seq(from = lim[1],to = lim[2]), 99), lim[2]))

dat <- runif(100, min = -10, max = 10)

dtrack <- DataTrack(data = dat, start = coords[-length(coords)],

                    end = coords[-1], chromosome = chr, genome = gen,

                    name = "Uniform")

plotTracks(list(itrack, gtrack, atrack, grtrack,

                 dtrack), from = lim[1], to = lim[2])

plotTracks(list(itrack, gtrack, atrack, grtrack,

                dtrack), from = lim[1], to = lim[2], type = "histogram")

3）Plotting parameters（画图参数调整）

3.1 设置参数

grtrack <- GeneRegionTrack(geneModels, genome = gen,

                           chromosome = chr, name = "Gene Model", transcriptAnnotation = "symbol",

                           background.title = "brown")

head(displayPars(grtrack))

plotTracks(list(itrack, gtrack, atrack, grtrack))

plotTracks(list(itrack, gtrack, atrack, grtrack),

           background.panel = "#FFFEDB", background.title = "darkblue")

3.2 Schemes（主题）

getOption("Gviz.scheme")

scheme <- getScheme()

scheme$GeneRegionTrack$fill <- "salmon"

scheme$GeneRegionTrack$col <- NULL

scheme$GeneRegionTrack$transcriptAnnotation <- "transcript"

addScheme(scheme, "myScheme")

options(Gviz.scheme = "myScheme")

grtrack <- GeneRegionTrack(geneModels, genome = gen,

                            chromosome = chr, name = "Gene Model")

plotTracks(grtrack)

options(Gviz.scheme = "default")

grtrack <- GeneRegionTrack(geneModels, genome = gen,

                           chromosome = chr, name = "Gene Model", transcriptAnnotation = "symbol")

3.3 Plotting direction （方向）

plotTracks(list(itrack, gtrack, atrack, grtrack),reverseStrand = TRUE)

4) Track classes

4.1 GenomeAxisTrack

axisTrack <- GenomeAxisTrack()

plotTracks(axisTrack, from = 1e+06, to = 9e+06)

axisTrack <- GenomeAxisTrack(range = IRanges(start = c(2e+06, 4e+06), end = c(3e+06, 7e+06), names = rep("N-stretch",+ 2)))

plotTracks(axisTrack, from = 1e+06, to = 9e+06)

 plotTracks(axisTrack, from = 1e+06, to = 9e+06, showId = TRUE)

plotTracks(axisTrack, from = 1e+06, to = 9e+06, add53 = TRUE,add35 = TRUE)

plotTracks(axisTrack, from = 1e+06, to = 9e+06, add53 = TRUE,

           add35 = TRUE, littleTicks = TRUE)

plotTracks(axisTrack, from = 1e+06, to = 9e+06, exponent = 4)

plotTracks(axisTrack, from = 1e+06, to = 9e+06, labelPos = "below")

 plotTracks(axisTrack, from = 1e+06, to = 9e+06, scale = 0.5)

plotTracks(axisTrack, from = 1e+06, to = 9e+06, scale = 0.5,

           labelPos = "below")

4.2) IdeogramTrack

ideoTrack <- IdeogramTrack(genome = "hg19", chromosome = "chrX")

plotTracks(ideoTrack, from = 8.5e+07, to = 1.29e+08)

plotTracks(ideoTrack, from = 8.5e+07, to = 1.29e+08,showId = FALSE)

plotTracks(ideoTrack, from = 8.5e+07, to = 1.29e+08,

           showId = FALSE, showBandId = TRUE, cex.bands = 0.5)

4.3 DataTrack

data(twoGroups)

dTrack <- DataTrack(twoGroups, name = "uniform")

plotTracks(dTrack)

plotTracks(dTrack, type = c("boxplot", "a", "g"))

总之，选择不同的画图参数，生成不同的图形

Data Grouping（对于分组数据）

plotTracks(dTrack, groups = rep(c("control", "treated"),

                                each = 3), type = c("a", "p", "confint"))

plotTracks(dTrack, groups = rep(c("control", "treated"),

                                each = 3), type = c("a", "p"), legend = TRUE)

data(dtHoriz)

dtHoriz <- dtHoriz[1:6, ]

plotTracks(dtHoriz, type = "horiz", groups = rownames(values(dtHoriz)),

           showSampleNames = TRUE, cex.sampleNames = 0.6,

           separator = 1)

总之，选择不同的图形参数类型，生成不同的图形类别

从数据文件中构建 DataTrack objects

bgFile <- system.file("extdata/test.bedGraph", package = "Gviz")

dTrack2 <- DataTrack(range = bgFile, genome = "hg19",

                       type = "l", chromosome = "chr19", name = "bedGraph")

plotTracks(dTrack2)

bamFile <- system.file("extdata/test.bam", package = "Gviz")

dTrack4 <- DataTrack(range = bamFile, genome = "hg19", type = "l", name = "Coverage", window = -1, chromosome = "chr1")

plotTracks(dTrack4, from = 189990000, to = 1.9e+08)

plotTracks(dTrack4, chromosome = "chr1", from = 189891483,to = 190087517)

Data transformations

dat <- sin(seq(pi, 10 * pi, len = 500))

dTrack.big <- DataTrack(start = seq(1, 1e+05, len = 500),

                         width = 15, chromosome = "chrX", genome = "hg19",

                         name = "sinus", data = sin(seq(pi, 5 * pi, len = 500)) *

                        runif(500, 0.5, 1.5))

plotTracks(dTrack.big, type = "hist")

plotTracks(dTrack.big, type = "hist", window = 50)

plotTracks(dTrack.big, type = "hist", window = -1,windowSize = 2500)

plotTracks(dTrack, groups = rep(c("control", "treated"),

                                 each = 3), type = c("b"), aggregateGroups = TRUE)

4.4 AnnotationTrack

aTrack <- AnnotationTrack(start = c(10, 40, 120),

                          width = 15, chromosome = "chrX", strand = c("+","*", "-"),

                          id = c("Huey", "Dewey", "Louie"),

                          genome = "hg19", name = "foo")

plotTracks(aTrack)

plotTracks(aTrack, shape = "box", featureAnnotation = "id")

plotTracks(aTrack, shape = "ellipse", featureAnnotation = "id", fontcolor.feature = "darkblue")

aTrack.groups <- AnnotationTrack(start = c(50, 180,260, 460, 860, 1240),

                                 width = c(15, 20, 40, 100,00, 20),

                                 chromosome = "chrX",

                                strand = rep(c("+", "*", "-"), c(1, 3, 2)),

                                group = rep(c("Huey", "Dewey", "Louie"), c(1, 3, 2)),

                                genome = "hg19",

                                name = "foo")                                                                                                                                                                   + "Dewey", "Louie"), c(1, 3, 2)), genome = "hg19",name = "foo")

plotTracks(aTrack.groups, groupAnnotation = "group")

plotTracks(aTrack.groups, groupAnnotation = "group",just.group = "above")

aTrack.stacked <- AnnotationTrack(start = c(50, 180,260, 800, 600, 1240), width = c(15, 20, 40, 100,

                                   500, 20), chromosome = "chrX", strand = "*",

                                  group = rep(c("Huey", "Dewey", "Louie"), c(1, 3, 2)),

                                  genome = "hg19", name = "foo")

plotTracks(aTrack.stacked, groupAnnotation = "group")

plotTracks(aTrack.stacked, stacking = "dense")

data("denseAnnTrack")

plotTracks(denseAnnTrack, showOverplotting = TRUE)

4.5,4.6,4.7,4.8,4.9回来再写

4.9 AlignmentsTrack

afrom <- 2960000

ato <- 3160000

alTrack <- AlignmentsTrack(system.file(package = "Gviz", "extdata", "gapped.bam"), isPaired = TRUE)

bmt <- BiomartGeneRegionTrack(genome = "hg19", chromosome = "chr12",start = afrom, end = ato, filter = list(with_ox_refseq_mrna = TRUE),stacking = "dense")

plotTracks(c(bmt, alTrack), from = afrom, to = ato, chromosome = "chr12")

plotTracks(c(bmt, alTrack), from = afrom, to = ato,

           chromosome = "chr12", min.height = 0, coverageHeight = 0.08,

           minCoverageHeight = 0)

plotTracks(c(alTrack, bmt), from = afrom, to = ato, chromosome = "chr12", type = "coverage")

plotTracks(c(bmt, alTrack), from = afrom + 12700,to = afrom + 15200, chromosome = "chr12")

plotTracks(c(bmt, alTrack), from = afrom + 12700,

          to = afrom + 15200, chromosome = "chr12", type = c("coverage","sashimi"))

introns <- GRanges("chr12", IRanges(start = c(2973662,2973919), end = c(2973848, 2974520)))

plotTracks(c(bmt, alTrack), from = afrom + 12700,

           to = afrom + 15200, chromosome = "chr12", type = c("coverage","sashimi"), sashimiFilter = introns)

plotTracks(c(bmt, alTrack), from = afrom + 12700,to = afrom + 15200, chromosome = "chr12",

           type = c("coverage", "sashimi"), sashimiFilter = introns, sashimiFilterTolerance = 5L)

plotTracks(c(bmt, alTrack), from = afrom + 12700,

           to = afrom + 15200, chromosome = "chr12", reverseStacking = TRUE,

            col.mates = "purple", col.gap = "orange", type = "pileup")

alTrack <- AlignmentsTrack(system.file(package = "Gviz","extdata", "gapped.bam"),isPaired = FALSE)

plotTracks(c(bmt, alTrack), from = afrom + 12700,to = afrom + 15200, chromosome = "chr12")

4.10 Creating tracks from UCSC data

from <- 65921878

to <- 65980988

knownGenes <- UcscTrack(genome = "mm9", chromosome = "chrX",

                         track = "knownGene", from = from, to = to, trackType = "GeneRegionTrack",

                        rstarts = "exonStarts", rends = "exonEnds", gene = "name",

                        symbol = "name", transcript = "name", strand = "strand",

                         fill = "#8282d2", name = "UCSC Genes")

refGenes <- UcscTrack(genome = "mm9", chromosome = "chrX",

                      track = "xenoRefGene", from = from, to = to,

                       trackType = "GeneRegionTrack", rstarts = "exonStarts",

                      rends = "exonEnds", gene = "name", symbol = "name2",

                       transcript = "name", strand = "strand", fill = "#8282d2",

                      stacking = "dense", name = "Other RefSeq")

ensGenes <- UcscTrack(genome = "mm9", chromosome = "chrX",

                       track = "ensGene", from = from, to = to, trackType = "GeneRegionTrack",

                       rstarts = "exonStarts", rends = "exonEnds", gene = "name",

                      symbol = "name2", transcript = "name", strand = "strand",

                      fill = "#960000", name = "Ensembl Genes")

cpgIslands <- UcscTrack(genome = "mm9", chromosome = "chrX",

                          track = "cpgIslandExt", from = from, to = to,

                          trackType = "AnnotationTrack", start = "chromStart",

                          end = "chromEnd", id = "name", shape = "box",

                          fill = "#006400", name = "CpG Islands")

snpLocations <- UcscTrack(genome = "mm9", chromosome = "chrX",

                          track = "snp128", from = from, to = to, trackType = "AnnotationTrack",

                           start = "chromStart", end = "chromEnd", id = "name",

                          feature = "func", strand = "strand", shape = "box",

                          stacking = "dense", fill = "black", name = "SNPs")

conservation <- UcscTrack(genome = "mm9", chromosome = "chrX",

                          track = "Conservation", table = "phyloP30wayPlacental",

                           from = from, to = to, trackType = "DataTrack",

                           start = "start", end = "end", data = "score",

                           type = "hist", window = "auto", col.histogram = "darkblue",

                           fill.histogram = "darkblue", ylim = c(-3.7, 4),

                           name = "Conservation")

gcContent <- UcscTrack(genome = "mm9", chromosome = "chrX",

                        track = "GC Percent", table = "gc5Base", from = from,

                        to = to, trackType = "DataTrack", start = "start",

                        end = "end", data = "score", type = "hist", window = -1,

                        windowSize = 1500, fill.histogram = "black",

                        col.histogram = "black", ylim = c(30, 70), name = "GC Percent")

axTrack <- GenomeAxisTrack()

idxTrack <- IdeogramTrack(genome = "mm9", chromosome = "chrX")

plotTracks(list(idxTrack, axTrack, knownGenes, refGenes,

                 ensGenes, cpgIslands, gcContent, conservation,

                 snpLocations), from = from, to = to, showTitle = FALSE)