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Circos: Circos Plot with R

Circos: Circos Plot with R. Henry Zhang, Ph.D. hzhang@mail.nih.gov Genetics Branch Center for Cancer Research National Cancer Institute. http://Circos.ca. Circos has been used and referenced in many scientific publications (501 as of October 2013).

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Circos: Circos Plot with R

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  1. Circos: Circos Plot with R Henry Zhang, Ph.D. hzhang@mail.nih.gov Genetics Branch Center for Cancer Research National Cancer Institute

  2. http://Circos.ca Circos has been used and referenced in many scientific publications (501 as of October 2013).

  3. Circos plot of somatic mutations, copy number variations, transcriptome expression, and structural variations. From inside to out, structural variations (purple and orange), copy number variations (gain in dark red, loss in dark blue, mRNA expression (up in gold, down in olive), differentially expressed microRNAs (up in red, down in green), DNA methylation with sky-blue background (up in dark orange, down in chartreuse), somatic mutations with a gene symbols, and chromosomal cytobands. Kim SC, Jung Y, Park J et al.2013 A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers PLoS One 8:e55596.

  4. > /usr//bin/CIRCOS/circos-0.60/bin/circos -conf mycircos.conf Circos plot: extra procedures are needed to prepare data files and configure file from dataset(s) <<include ideogram.conf>> <image> <<include etc/image.conf>> </image> . . <plots> <plot> file = data/6/snp.density.50kb.txt color = black r0 = 1.075r r1 = 1.15r . . </plot> <plot> file = data/6/snp.number.50kb.txt color = black r0 = 0.85r r1 = 0.95r . . </plot> </plots> . . . hsY 0 49999 0.00804 hsY 50000 99999 0.0033 hsY 100000 149999 0.0084 hsY 150000 199999 0.00316 hsY 200000 249999 0.007 hsY 250000 299999 0.00466 hsY 300000 349999 0.00636 hsY 350000 399999 0.00576 hsY 400000 449999 0.00678 hsY 450000 499999 0.00688 hsY 0 49999 402 hsY 50000 99999 165 hsY 100000 149999 420 hsY 150000 199999 158 hsY 200000 249999 350 hsY 250000 299999 233 hsY 300000 349999 318 hsY 350000 399999 288 hsY 400000 449999 339 hsY 450000 499999 344

  5. R Bioconductor package: ggbio • Requires ggplot2, biovizBase, and GenomicRanges packages • All data are held with GRange object • All plots are wrapped into one function. • Plots are arranged in layers • Parameters must be correctly selected (Yin, T. et al: Genome Biology 2012, 13:R77)

  6. layout_circle() in ggbio package: a complicated function with some unimplemented plot functionalities layout_circle(data, ..., geom = c("point", "line", "link", "ribbon", "rect", "bar", "segment", "hist", "scale", "heatmap", "ideogram", "text"), linked.to, radius = 10, trackWidth = 5, space.skip = 0.015, direction = c("clockwise", "anticlockwise"), link.fun = function(x, y, n = 30) bezier(x, y, evaluation = n), rect.inter.n = 60, rank, ylim = NULL, scale.n = 60, scale.unit = NULL, scale.type = c("M", "B", "sci"), grid.n = 5, grid.background = "gray70", grid.line = "white", grid = FALSE, chr.weight = NULL)

  7. An R package implementing Circos 2D track plot Implemented in pure R and relies on only R packages that came with R base installation. Provides a set of graphic functions and each plot type, such as scatter, line, histogram, heatmap, tile, connectors, links (lines and ribbons ), and text (gene) labels, has its own function . Use R low level R graphics functions only. Availability: http://www.r-project.org Reference: Hongen Zhang, Paul Meltzer and Sean Davis (2013): RCircos: an R package for Circos 2D track plots. BMC Bioinformatics 14:244

  8. easy to use

  9. easy to use Basic steps to generate an RCircos plot image: Load RCircos library Load chromosome cytoband data Setup RCircos core components Load input data Open graphic device Call specific plot function to plot each data track (chromosome ideogram, gene names, heatmap, scatter plot, ….) Close the graphic device if it is image file (Graphic device could be R GUI, Tiff, PNG, and PDF files).

  10. supports multiple ideogram data

  11. use data frame for input data Input data format for heatmap, histogram, scatterplot, line plot, gene label, connector, and tile: Input data format for links:

  12. use data frame for input data

  13. easy to integrate with other R graphic functions Mouse and rat chromosome ideograms, heatmaps, and link lines are drawn with RCircos with two input datasets. Title, legend, and color key are added with function calls of R graphics package.

  14. Step 1: decide how many data tracks and where you will plot them RCircos follows the layout paradigm set forth by Circos and arranges data plots by tracks. The core track is the chromosome ideogram track with highlighting and labels. Data plot tracks can be placed inside or outside of chromosome ideogram track.

  15. Step 2: Load cytoband data and setup RCircos core components Plot with all chromosomes: If plot only some chromosomes:

  16. Step 3: modify plot parameter if necessary

  17. Step 4: load input datasets Step 5: open graphic device Types of graphic devices than Rcircos supports: R GUI, files of png, pdf, tiff png(file="RCircos.Demo.Human.png", height=8, width=8, unit="in", type=“windows", res=300); tiff(file="RCircos.Demo.Human.tif", height=8, width=8, unit="in", type=" windows ", res=300); pdf(file="RCircos.Demo.Human.pdf", height=8, width=8); (If using image files, graphic device must be closed after plot is done). RCircos.Set.Plot.Area(); or if you want control the size of plot area par(mai=c(0.25, 0.25, 0.25, 0.25)); plot.new(); plot.window(c(-1.5, 1.5), c(-1.5, 1.5));

  18. Step 6: plot chromosome ideogram and data tracks RCircos.Chromosome.Ideogram.Plot() RCircos.Heatmap.Plot(heatmap.data, data.col=6, track.num=5, side="in") RCircos.Gene.Connector.Plot(gene.data, track.num=1, side="in") RCircos.Gene.Name.Plot(gene.data, Name.col=4, track.num=2, side="in") RCircos.Tile.Plot(tile.data, track.num=9, side="in") RCircos.Line.Plot(line.data, data.col= 4, track.num=7, side="in") RCircos.Link.Plot(link.data, track.num=11, by.chromosome=FALSE); RCircos.Histogram.Plot(hist.data, data.col=4, track.num=6, side="in") RCircos.Ribbon.Plot(ribbon.data, track.num =10, by.chromosome=FALSE, twist =FALSE) RCircos.Scatter.Plot(scatter.data, data.col=5, Track.num=8, side="in", by.fold=1)

  19. RCircos core component: RCircos plot parameters track.padding track.out.start highlight.pos track.in.start chr.name.pos track.height chr.ideog.pos chrom.width chrom.paddings

  20. RCircos core component: RCircos plot positions

  21. RCircos core component: RCircos plot ideograms

  22. Customizing heatmap plot colors

  23. Customizing other plot colors by appending A column of color names to input dataset

  24. Add more decorations

  25. Adjust plot range

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