News

Changes in version 0.4.5

• vertical lines added for y-axis.
• add axis.labels.cex and labels.cex in circos.genomicInitialize().
• remove lwd in circos.genomicRect() because lwd is not allowed to be vector.
• fixed a bug when self.link = 1 in chordDiagram()
• add scale in chordDiagram()
• circos.initialize(): convert xlim and x to numeric
• colorRamp2() is faster now.
• add circos.genomicAxis().
• add calc_gap().
• chordDiagram(): consider tibble format as input.

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