Circular Visualization

Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data.


News

Changes in version 0.4.4

  • update denpendency of GlobalOptions package
  • genomicDensity(): add chr.len argument.

Changes in version 0.4.3

  • circos.trackHist(): add area argument to add filled color under density lines.
  • getColorInfo(): use ls(envir) to get the names of variables in the environment.
  • circos.arrows: add instructions of making reverse clockwise arrows.

Changes in version 0.4.2

  • add startup message
  • add xmax argument in chordDiagram()
  • first column is refactorized in circos.initialize()
  • add names for CELL_META
  • add labels.pos.adjust in circos.axis()
  • add fontsize() function
  • circos.nested(): check whether sector order in the two circular plots are consistent
  • getQuadraticPoints(): add tiny offset when the curve is actually a straight line

Changes in version 0.4.1

  • add circos.raster()
  • add circos.arrow()
  • re-implement rand_color()
  • support col in circos.axis()
  • circos.genomicLabels(): regions are automatically sorted in advance

Changes in version 0.4.0

  • add link.visible argument in chordDiagram()
  • add cytoband files and chromInfo files for a list of species locally
  • add a new vignette "Add legends to circlize"
  • add a new function convert_*() which convert an absolute unit to measurement in different coordinates
  • enforce asp = 1 when calling plot.default
  • length of axes ticks are set to 2mm by default
  • in axis, the first axis label is shifted if it is exceed the axis and so is for the last axis label.
  • text.vjust accepts strings as "2mm", "-2.1 cm" to represent offsets
  • circos.segments(): graphic parameters can be set as vectors
  • add circos.genomicIdeogram(), circos.genomicHeatmap(), circos.genomicLabels()
  • add circos.nestes()
  • vignette has been moved to http://jokergoo.github.io/circlize_book/book/index.html
  • add set.current.cell()
  • add h.ratio argument in circos.link()

Changes in version 0.3.10

  • chordDiagram(): fixed a bug when the input matrix is stored as a data frame
  • rainfallTransform(): add "left" and "right" modes, and now the row order of the output data frame is as same as the input one.
  • circos.genomicInitialize(): it can only plot axes now.
  • posTransform.text(): add extend option to control the extension of chromsomes to allow to put more labels
  • ciros.points(): add bg option to control background color

Changes in version 0.3.9

  • chordDiagramFromDataFrame(): now recognize a rank column which defines the order of adding links

Changes in version 0.3.8

  • chordDiagram(): if not all sectors are specified in grid.col, remaining will be filled by random colors
  • if ylim has same values for upper and lower bound, throw errors.

Changes in version 0.3.7

  • chordDiagram() now returns a data frame which contains positions of all links
  • chordDiagram() track.margin is also taken into settings of preAllocateTracks
  • chordDiagram(): link.sort adds a new option: "overall" which sort links regardless of rows or columns
  • chordDiagram(): add link.largest.ontop which controls the order of adding links

Changes in version 0.3.6

  • positions of arrows in chordDiagram() have been adjusted.
  • fixed a bug that negative value was not shown
  • circos.initialize: if factors are unique and is a vector, the order of sectors will be the same as factors.
  • highlight.sector: text are now in correct position if sectors are over theta = 0

Changes in version 0.3.5

  • chordDiagram(): if the corresponding value is zero, nothing happens.
  • border of links are same as filled by default
  • explicitely put all arguments in chordDiagram() instead of just using ...
  • adj in circos.text() can also adjust text rotations.
  • 'circos.genomicInitialize()': gap between labels and ideograms is adjusted if there is no axis

Changes in version 0.3.4

  • circos.genomicLink(): ordering is cancled when normalizing the data frames
  • export smartAlign()

Changes in version 0.3.3

  • rainfallTransform() and genomicDensity(): can be applied on the bed-format data frame directly.
  • add col2rgb() which transforms back to the original value based on the color mapping function.
  • add circos.yaxis()

Changes in version 0.3.2

  • chrodDiagram: add warning if users use data frame as ajacency matrix
  • circos.genomicTrackPlotRegion: data frame will be sorted

Changes in version 0.3.1

  • fixed a bug for chordDiagramFromDataFrame when there is the third column in the data frame
  • colorRamp2: colors are interpolated linearly in Lab color space
  • chordDiagram: directional, direction.type and diffHeight can also be vector

Changes in version 0.3.0

  • chordDiagramFromMatrix: automatically replace NA to 0 in the input matrix
  • add chordDiagramFromMatrix and chordDiagramFromDataFrame
  • by default there is axis on chord diagram
  • add quadratic.bezier.length that calculates the approximate length of bezier curve
  • normalize link-related functions to make sure the direction is always from the first argument to the second argument, reverse clockwise.

Changes in version 0.2.5

  • circos.rect and circos.polygon are vectorized
  • circos.dendrogram: supports graphical settings for nodes
  • circos.link: support 'big.arrow' mode for links
  • circos.text: graphical settings are subsetted correctly in niceFacing is set
  • add shortcut functions: circos.track, circos.update and circos.genomicTrack
  • add normalizeChordDiagramGap
  • fixed type in get.cell.meta.data

Changes in version 0.2.4

  • 'chrodDiagram`: If graphic parameters for links are different, the value can be specified as a three-column data frame.
  • chordDiagram: arrows can be used to identify directions
  • ¬∑circos.link`: arrows can be used to identify directions
  • chordDiagram: width of self-links are not duplicated.
  • circos.link: if two roots for a link overlaps, the link is de-generated as an area with a quadratic curve and an arc.
  • add circos.dendrogram which draw dendrograms (dendrogram can be rendered by dendextend package)

Changes in version 0.2.3

  • add link.order argument in chordDiagram to control order of links on sectors
  • add highlight.sector
  • chromosome.index can set the order of chromosomes
  • add read.chromInfo() to read chromInfo file from UCSC
  • if downloading cytoband file failed, try to download chromInfo file
  • chromosome.index can be set in read.cytoband() and read.chromInfo()

Changes in version 0.2.2

  • change .onLoad to setLoadActions
  • circos.clear: tempdir will not be reset

Changes in version 0.2.1

  • If par("mar") is using default, it will be changed to par(mar = c(1, 1, 1, 1)) internally and will be recovered after calling circos.clear()
  • circos.text: add two options ('bending.inside' which is identical to original 'bending' and 'bending.outside'), both support niceFacing
  • circos.par('tempdir') is initialized by tempdir()
  • .get_color: there will be no negative value due to 0.000 - 0.000
  • chordDiagram: grid.col is correctly reduced if rownames and colnames overlap
  • circos.text: font is passed to text function
  • colorRamp2: returned function has an attribute: breaks
  • chordDiagram: assign same names for rows and columns if the input matrix is specified symmetric while has no names
  • chordDiagram: also check rownames and colnames if the matrix is specified as symmetric.
  • don't remove temporary folder
  • value can be scalar or vector in circos.genomicPoints, circos.genomicLines, ...

Changes in version 0.2.0

  • draw.sector is modified, now accepts an argument clock.wise to control the direction of sectors.
  • highlight.chromosome can highlight more than one chromosomes now.
  • vignettes are rendered by knitr
  • set default transparency to 0.5 in chordDiagram
  • circlize returns value when track.index == 0
  • fixed a bug when text facing is 'bending', all text are plotted in one cell
  • different colors for each rows can be set to circos.genomicLines if type %in% c("segment", "h")
  • pre-allocate the matrix in .get_color

Changes in version 0.1.3

  • add jitter for adding points under stack mode
  • value in panel.fun can be selected by character index
  • change default temporary dir to tempdir()

Changes in version 0.1.3

  • temporary add dependency of methods until bugs in GlobalOptions fixed
  • add reduce argument in chordDiagram to control whether to remove tiny categories
  • add species argument in generateRandomBed
  • change use of posTransform.text
  • add names for chr.len in read.cytoband
  • cytoband files are cached
  • row.col, column.col, col, grid.col and circos.par('gap.degree') will also be reduced if the matrix is reduced

Changes in version 0.1.2

  • global options are controlled by GlobalOptions package
  • set par("lend") and par("ljoin") to their default values.
  • add more example codes in genomic_plot vignette

Changes in version 0.1.1

  • fixed the bug that if start position is not zero when calling circos.genomicIntialize, major.at is wrongly calculated.

Changes in version 0.1.0

  • height(h) and shape(w) can be set for Bezier curve (in circos.link)
  • add examples in man/
  • add fromRows options in chordDiagram to control the direction of links
  • Now the major.by are the same in all sectors
  • define min.data and max.data in internal variable SECTOR.DATA
  • check that sector names cannot be empty strings ("")
  • check whether circos plot has been initialized when calling circos.trackPlotRegion
  • add niceFacing in circos.text to make the facing more human easy
  • height of ideogram and annotation track in circos.initializeWithIdeogram and circos.genomicInitialize can be set
  • some example code in examples/vignettes has been changed according to changes in the package source code
  • add posTransform.text which can smartly put text on the circle
  • track.margin and cell.padding can be set in circos.trackPlotRegion as a local setting

Changes in version 0.0.9

  • links are now implemented by Bezier curve
  • baseline can be set when type == "h" in circos.lines
  • add a new function chordDiagram which support chord diagram
  • add facing argument to replace direction in circos.text
  • circos.trackPlotRegion can be used to update a track without re-setting ylim
  • move demo to http://jokergoo.github.io/circlize
  • re-implement colorRamp2

Changes in version 0.0.8

  • axes labels will not draw when setting labels = FALSE
  • add many functions supporting genomic visualization
  • add a new vignette to show how to plot genomic circos plot with new functions
  • add circos.info

Changes in version 0.0.7

  • add an example in demo codes
  • improved vignettes

Change in version 0.0.6

  • order will not change in circos.trackPlotRegion when not specifying factors, bug fixed
  • add an example in 'draw relation' vignette
  • add a new vignette focusing on phylogenetic tree
  • support directly downloading cytoBand file from UCSC

Changes in version 0.0.5

  • support self-define width of sectors when initializing sectors
  • add simple functions to read and manuplate cytoband file
  • add several new figures in the vignettes and vignettes have been improved.
  • cell.padding in circos.par now using degree as its measurement.
  • track.margin in circos.par now using percentage of radius as its measurement.

Changes in version 0.0.4

  • number of points to simulate quadratic curves decreased
  • labels on axis in circos.initializeWithIdeogram is now 'vertical_right' by default
  • size of the vignettes reduced
  • add example of drawing heatmap and cluster dendrogram in the main vignette
  • add example of drawing error area of lines by circos.polygon
  • vignette improved
  • gap.degree in circos.par can be a vector which means different degrees for gaps can be set
  • export core function circlize now
  • track.margin now is in correct order
  • links are optimized (although not so perfect)
  • no point overflow warnings when drawing axes

Changes in version 0.0.3

  • vignettes has been improved
  • xplot in get.cell.meta.data is now corresponding to the data direction in the cell
  • number of points to draw links decreased.
  • get.cell.meta.data can provide more meta data for a cell
  • start degree and end degree now consistent with the data axis.
  • the first sector is drawn first now.
  • add draw.sector

Changes in version 0.0.2

  • add draw.sector so it would be more straightforward to highlight sectors
  • add track.margin, cell.padding, cell.xlim and cell.ylim in get.cell.meta.data function
  • figures in vignettes are all generated automatically
  • vignettes have been imporved

Reference manual

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