RCircos包绘制染色体模式图

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RCircos包绘制染色体模式图

2024-07-09 09:20| 来源: 网络整理| 查看: 265

## 1.设置当前工作目录

setwd("./RCircos")

## 2.安装和导入R包：RCircos

# install.packages("RCircos")

library("RCircos")

## 3.RCircos包简要信息 ### 3.1 DESCRIPTION

# Package: RCircos

# Type: Package

# Title: Circos 2D Track Plot

# Version: 1.2.1

# Date: 2019-03-10

# Author: Hongen Zhang

# Maintainer: Hongen Zhang

# Description: A simple and flexible way to generate Circos 2D track plot images for genomic data visualization is implemented in this package. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.

# License: GPL (>= 2)

# Depends: R (>= 2.10)

# URL: http://bitbucket.org/henryhzhang/rcircos

# NeedsCompilation: no

# Packaged: 2019-03-12 16:32:41 UTC; hzhang

# Repository: CRAN

# Date/Publication: 2019-03-12 21:06:27 UTC

# Built: R 3.6.0; ; 2019-05-28 21:23:44 UTC; windows

### 3.2 MAIN FUNCTION

ls(package:RCircos)

# [1] "RCircos.Adjust.Scatter.Values"

# [2] "RCircos.Area.Highlight"

# [3] "RCircos.Area.Plot"

# [4] "RCircos.Chromosome.Ideogram.Plot"

# [5] "RCircos.Clear.Track"

# [6] "RCircos.Clear.Zoom.Area"

# [7] "RCircos.Customized.Connection.Plot"

# [8] "RCircos.Customized.Shape.Plot"

# [9] "RCircos.Data.Point"

# [10] "RCircos.defaultBasePerUnits"

# [11] "RCircos.defaultCharWidth"

# [12] "RCircos.defaultChromPadding"

# [13] "RCircos.defaultCircosUnits"

# [14] "RCircos.defaultTextSize"

# [15] "RCircos.Draw.Chromosome.Ideogram"

# [16] "RCircos.Env"

# [17] "RCircos.Gene.Connector.Plot"

# [18] "RCircos.Gene.Name.Plot"

# [19] "RCircos.Get.Arrow.Shape"

# [20] "RCircos.Get.Chromosome.Order"

# [21] "RCircos.Get.Data.Point.Height"

# [22] "RCircos.Get.Default.Base.Per.Units"

# [23] "RCircos.Get.Default.Char.Width"

# [24] "RCircos.Get.Default.Chrom.Padding"

# [25] "RCircos.Get.Default.Circos.Units"

# [26] "RCircos.Get.Default.Text.Size"

# [27] "RCircos.Get.Gene.Label.Locations"

# [28] "RCircos.Get.Gene.Name.Plot.Parameters"

# [29] "RCircos.Get.Heatmap.Color.Scale"

# [30] "RCircos.Get.Heatmap.Color.Scale.Location"

# [31] "RCircos.Get.Heatmap.Data.Colors"

# [32] "RCircos.Get.Link.Colors"

# [33] "RCircos.Get.Padding.Constant"

# [34] "RCircos.Get.Paired.Points.Positions"

# [35] "RCircos.Get.Plot.Boundary"

# [36] "RCircos.Get.Plot.Colors"

# [37] "RCircos.Get.Plot.Ideogram"

# [38] "RCircos.Get.Plot.Layers"

# [39] "RCircos.Get.Plot.Parameters"

# [40] "RCircos.Get.Plot.Positions"

# [41] "RCircos.Get.Polygon.Height"

# [42] "RCircos.Get.Single.Point.Positions"

# [43] "RCircos.Get.Start.End.Locations"

# [44] "RCircos.Get.Supported.HeatmapColors"

# [45] "RCircos.Get.Supported.Plot.Types"

# [46] "RCircos.Get.Track.Positions"

# [47] "RCircos.Get.Zoom.Data"

# [48] "RCircos.Get.Zoom.Range"

# [49] "RCircos.Heatmap.Plot"

# [50] "RCircos.heatmapColors"

# [51] "RCircos.Highligh.Chromosome.Ideogram"

# [52] "RCircos.Histogram.Plot"

# [53] "RCircos.Ideogram.Tick.Plot"

# [54] "RCircos.Initialize.Plot.Parameters"

# [55] "RCircos.Label.Chromosome.Names"

# [56] "RCircos.Label.Zoom.Region"

# [57] "RCircos.Line.Plot"

# [58] "RCircos.Link.Line"

# [59] "RCircos.Link.Plot"

# [60] "RCircos.List.Plot.Parameters"

# [61] "RCircos.Mark.Zoom.Area"

# [62] "RCircos.Multiple.Species.Core.Components"

# [63] "RCircos.Multiple.Species.Dataset"

# [64] "RCircos.paddingConst"

# [65] "RCircos.Parallel.Line.Plot"

# [66] "RCircos.Plot.Heatmap.Color.Scale"

# [67] "RCircos.Plot.Zoomed.Area"

# [68] "RCircos.Plot.Zoomed.Continue.Lines"

# [69] "RCircos.Plot.Zoomed.Gene.Connectors"

# [70] "RCircos.Plot.Zoomed.Heatmap"

# [71] "RCircos.Plot.Zoomed.Histogram"

# [72] "RCircos.Plot.Zoomed.Ideogram.Ticks"

# [73] "RCircos.Plot.Zoomed.Parallel.Lines"

# [74] "RCircos.Plot.Zoomed.Polygons"

# [75] "RCircos.Plot.Zoomed.Scatters"

# [76] "RCircos.Plot.Zoomed.Tiles"

# [77] "RCircos.Plot.Zoomed.Vertical.Lines"

# [78] "RCircos.plotTypes"

# [79] "RCircos.Point.Plot"

# [80] "RCircos.Polygon.Plot"

# [81] "RCircos.Pseudo.Ideogram.From.Labels"

# [82] "RCircos.Pseudo.Ideogram.From.Table"

# [83] "RCircos.Reset.Plot.Ideogram"

# [84] "RCircos.Reset.Plot.Parameters"

# [85] "RCircos.Reset.Plot.Positions"

# [86] "RCircos.Ribbon.Plot"

# [87] "RCircos.Scatter.Plot"

# [88] "RCircos.Set.Base.Plot.Positions"

# [89] "RCircos.Set.Core.Components"

# [90] "RCircos.Set.Cytoband.Data"

# [91] "RCircos.Set.Plot.Area"

# [92] "RCircos.Set.Zoom.Plot.Positions"

# [93] "RCircos.Sort.Genomic.Data"

# [94] "RCircos.Tile.Plot"

# [95] "RCircos.Track.Outline"

# [96] "RCircos.Validate.Cyto.Info"

# [97] "RCircos.Validate.Genomic.Data"

# [98] "RCircos.Validate.Genomic.Info"

# [99] "RCircos.Validate.Plot.Parameters"

# [100] "RCircos.Validate.Track.Positions"

# [101] "RCircos.Vertical.Line.Plot"

# [102] "RCircos.Workflow"

# [103] "RCircos.Zoom.Area.Outline"

# [104] "RCircos.Zoom.Paired.Plot.Positions"

# [105] "RCircos.Zoom.Single.Plot.Positions"

# [106] "RCircos.ZoomIn.Chromosome"

# [107] "RCircos.ZoomOut.Chromosome"

## 4.导入测试数据以及绘制复合染色体模式图（Circos）

#@ 导入测试数据

data(RCircos.Histogram.Data)

head(RCircos.Histogram.Data)

# Chromosome chromStart chromEnd Data

# 1 chr1 45000000 49999999 0.070859

# 2 chr1 55000000 59999999 0.300460

# 3 chr1 60000000 64999999 0.125421

# 4 chr1 70000000 74999999 0.158156

# 5 chr1 75000000 79999999 0.163540

# 6 chr1 80000000 84999999 0.342921

data(RCircos.Heatmap.Data)

head(RCircos.Heatmap.Data)

# Chromosome chromStart chromEnd GeneName X786.O A498

# 1 chr1 934341 935552 HES4 6.75781 7.38773

# 2 chr1 948846 949919 ISG15 7.56297 10.49590

# 3 chr1 1138887 1142089 TNFRSF18 4.69775 4.55593

# 4 chr1 1270657 1284492 DVL1 7.76886 7.52194

# 5 chr1 1288070 1293915 MXRA8 4.49805 4.72032

# 6 chr1 1592938 1624243 SLC35E2B 8.73104 8.10229

# A549.ATCC ACHN BT.549 CAKI.1

# 1 6.47890 6.05517 8.85062 7.00307

# 2 5.89893 7.58095 12.08470 7.81459

# 3 4.38970 4.50064 4.47525 4.47721

# 4 6.87125 7.03517 7.65386 7.69733

# 5 4.62207 4.58575 5.66389 4.93499

# 6 8.36599 9.04116 9.24175 9.89727

data(RCircos.Link.Data)

head(RCircos.Link.Data)

# Chromosome chromStart chromEnd Chromosome.1 chromStart.1

# 1 chr1 8284703 8285399 chr1 8285752

# 2 chr1 85980143 85980624 chr7 123161313

# 3 chr1 118069850 118070319 chr1 118070329

# 4 chr1 167077258 167077658 chr1 169764630

# 5 chr1 171671272 171671550 chr1 179790879

# 6 chr1 174333479 174333875 chr6 101861516

# chromEnd.1

# 1 8286389

# 2 123161687

# 3 118070689

# 4 169764965

# 5 179791292

# 6 101861840

data(UCSC.HG19.Human.CytoBandIdeogram);

head(UCSC.HG19.Human.CytoBandIdeogram);

# Chromosome ChromStart ChromEnd Band Stain

# 1 chr1 0 2300000 p36.33 gneg

# 2 chr1 2300000 5400000 p36.32 gpos25

# 3 chr1 5400000 7200000 p36.31 gneg

# 4 chr1 7200000 9200000 p36.23 gpos25

# 5 chr1 9200000 12700000 p36.22 gneg

# 6 chr1 12700000 16200000 p36.21 gpos50

data(UCSC.Mouse.GRCm38.CytoBandIdeogram);

head(UCSC.Mouse.GRCm38.CytoBandIdeogram);

# Chromosome ChromStart ChromEnd Band Stain

# 1 chr1 0 8840440 qA1 gpos100

# 2 chr1 8840440 12278390 qA2 gneg

# 3 chr1 12278390 20136559 qA3 gpos33

# 4 chr1 20136559 22101102 qA4 gneg

# 5 chr1 22101102 30941543 qA5 gpos100

# 6 chr1 30941543 43219933 qB gneg

data(UCSC.Baylor.3.4.Rat.cytoBandIdeogram);

head(UCSC.Baylor.3.4.Rat.cytoBandIdeogram);

# Chromosome ChromStart ChromEnd Band Stain

# 1 chr1 0 10142096 p13 gneg

# 2 chr1 10142096 24272657 p12 gvar

# 3 chr1 24272657 38517175 p11 gneg

# 4 chr1 38517175 48659271 q11 gpos

# 5 chr1 48659271 69741157 q12 gneg

# 6 chr1 69741157 90025350 q21 gpos

chr.exclude

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RCircos包绘制染色体模式图

RCircos包绘制染色体模式图

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