NEWS

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circlize 0.4.16 (2024-02-20)

• fixed a bug caused by comparing two floating numbers under "ring " mode.
• fixed a bug where 'direction.type' was wrongly used as a vector.
• 'chordDiagram()': if the input is a character matrix, convert it to a data frame.
• 'circos.heatmap()': add a new function 'circos.heatmap.get.x()' which calculates the x-positions on sectors for original matrix rows.
• 'circos.initializeWithIdeogram()': add a new argument 'draw.chr.prefix'.
• add 'circos.stacked_text()'.
• 'posTransform.text()': the coordinates are now based on cell.xlim while not xlim.
• 'circos.rect()': support round rect.

circlize 0.4.15 (2022-05-10)

• low-level graphics functions won't change the index of sector and track.
• 'colorRamp2()': add 'hcl_palette' argument.
• 'highlight.sectors()': argument 'padding' supports to wrap the vector with 'I()'.
• fixed a bug of wrong calculation of label positions in 'circos.genomicLabels()'.

circlize 0.4.14 (2022-02-11)

• 'circos.genomicTrackPlotRegion()': add 'na.rm = TRUE' when using 'range()'.
• fixed a bug of 'na.col' in 'circos.heatmap()'.
• improved default order of link end when duplicated rows exist in the data frame.
• 'circos.heatmap()': add 'cell.border', 'cell.lty' and 'cell.lwd' arguments.
• add 'circos.initializeCircularGenome()'.
• 'chordDiagram()': 'link.sort' allows to sort links based on the original orders in the input data frame.
• label facing is correct now for y-axis when circos.par$xaxis.clock.wise is FALSE.
• 'rand_color()': add a new argument 'friendly' that generate eye-friendly random colors.
• 'chordDiagram()': fixed a bug when a sector have all zero values and after scaling they changed to NA.

circlize 0.4.13 (2021-06-09)

• 'circos.link()': add offset when testing whether the link is out of the sector.

circlize 0.4.12 (2021-01-08)

• 'smartAlign()': improved boxes overlapping
• 'circos.heatmap()': automatically convert the input to a matrix if it is a data frame
• now validate the regions to check whether the regions are exceeding the chromosomes.
• 'circos.link()': add a new 'inverse' argument to control whether the link is inversed or not.
• 'circos.genomicLabels()': replace 'side' argument with 'labels.side'.
• 'circos.points()', 'circos.lines()', 'circos.text()' allow argument 'x' to be a two-column matrix.
• add 'arrange_links_evenly()' function.
• add 'circos.connect()' function.
• 'circos.heatmap()': argument 'cluster' can be a clustering object.
• 'circos.heatmap()': add 'cell_width' to control the relative width of heatmap cells.
• add 'circos.labels()'.
• 'chordDiagram()': bars are drawn according to the visibility of links.

circlize 0.4.11 (2020-10-31)

• 'chordDiagram()': add 'link.auto' argument
• 'chordDiagram()': add 'link.target.prop' and 'target.prop.height' arguments
• 'circos.par()': add 'circle.margin' option
• 'circos.genomicLabels()': fixed a bug when 'direction = "outside"'
• add 'xaxis.clock.wise' option in 'circos.par()'
• 'chordDiagram()': now the scaling is properly applied.
• 'chordDiagram()': link positions are optimized so they have minimal intersections. 'link.auto' argument is ignored and removed.
• 'circos.dendrogram()': support arbitary numbers of branches on each node.
• all functions with 'factors' with arguments change to 'sectors'.

circlize 0.4.10 (2020-06-14)

• 'highlight.sector()': fixed a bug when circos.par("clock.wise" = FALSE)
• 'circos.genomicLink()': input data frames can have 2 columns. In this case the start and the end positions of each region are the same.
• 'circos.circos.trackPlotRegion()': fixed a bug that sector index was wrongly assigned.
• 'get.cell.meta.data()': add 'cell.width' and 'cell.height' arguments.
• 'circos.genomicTrackPlotRegion()': when input is a data frame list and column.index is a vector, reduce the one-column data frame to a vector.
• add 'add.track.meta.data()' and 'add.sector.meta.data()' too add user-defined cell meta data.
• add 'circos.heatmap()' to draw multi-track heatmaps.
• add 'circos.barplot()', 'circos.boxplot()' and 'circos.violin()'.
• sector index are all enforced to be character.
• 'circos.nested()': now the graphic parameters are reordered accordingly as the 'correspondance'.
• add 'mm_x()', 'mm_y()', 'mm_h()', 'cm_x()', 'cm_y()', 'cm_h()', 'inches_x()', 'inches_y()', 'inches_h()' functions
• 'circos.initialize():' if 'gap.degree'/'gap.after' is set a named vector, the order of these two options are adjusted to the real sector order.
• add 'set_track_gap()' function.
• 'circos.link()': add 'reduce_to_mid_line' argument.
• 'chordDiagram()': add 'group' argument.

circlize 0.4.9 (2020-04-30)

• 'chordDiagram()': fixed a bug when 'link.overlap = TRUE' for sparse matrices.
• 'circos.rect()': add 'rot' argument.
• add 'circos.triangle()'.
• all examples are included in R source code files
• 'circos.genomicHeatmap()': 'connection_height' can be set to 'NULL' to remove the connection lines.
• 'genomicDensity()'/'circos.genomicDensity()': add a new 'count_by' argument so that the overlap can be calculated as how many regions overlap to the windows.
• 'circos.trackPlotRegion()': cells in all sectors are plotted if 'fa' does not provide complete set of categories.
• 'circos.initialize()': give warnings if 'fa' is in numeric mode.
• 'circos.track()'/'circos.genomicTrack()': gives error when the panel function was specified without explicitly by the name 'panel.fun'.
• 'chordDiagram()': if the input is a data frame, it allows the data frame to have two numeric columns and the link ends are drawn wiht unequal width.

circlize 0.4.8 (2019-09-08)

• add 'validate_regions()' to check the end positions and start positions.
• 'colorRamp2()': fixed a bug when the color mapping function returns RGB matrix.
• 'circos.genomicHeatmap()': add 'na_col' argument.
• 'chordDiagram()': add 'link.overlap' argument.

circlize 0.4.7 (2019-08-21)

• fixed a bug that the vertical line was wrongly put for 'circos.yaxis()'.
• validate input if it is should be a data frame.
• 'colorRamp2()': add HLS colorspace
• add 'major.at' and 'labels' arguments to 'circos.genomicAxis()'.
• circos.initializeWithIdeogram(): manually select chromosomes for the common species
• 'chordDiagram()': fixed a bug that after reducing the matrix/data frame by 'reduce', there might be sectors with zero width.
• optimized 'circos.nested()'
• 'colorRamp2()': check NA values

circlize 0.4.6 (2019-04-03)

• smartAlign(): the order of values won't affect the realignment now.
• 'circos.rect()', 'circos.segments()', 'circos.points()', 'circos.text()': x and y are recycled if the length of the variable is 1.
• fixed a bug of the position of vertical line in 'circos.yaxis()'
• add 'facing' and 'niceFacing' to 'circos.genomicLabels()'
• 'posTransform.text()': linking lines will not be overlapping anymore.

circlize 0.4.5 (2018-11-21)

• 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.

circlize 0.4.4 (2018-06-10)

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

circlize 0.4.3 (2017-12-20)

• '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.

circlize 0.4.2 (2017-11-18)

• 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

circlize 0.4.1 (2017-07-19)

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

circlize 0.4.0 (2017-05-29)

• 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 https://jokergoo.github.io/circlize_book/book/index.html
• add 'set.current.cell()'
• add 'h.ratio' argument in 'circos.link()'

circlize 0.3.10 (2017-03-07)

• '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

circlize 0.3.9 (2016-09-26)

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

circlize 0.3.8 (2016-08-14)

• 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.

circlize 0.3.7 (2016-05-15)

• 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

circlize 0.3.6 (2016-04-23)

• 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

circlize 0.3.5 (2016-03-28)

• '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

circlize 0.3.4 (2015-12-22)

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

circlize 0.3.3 (2015-11-26)

• '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()'

circlize 0.3.2 (2015-10-21)

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

circlize 0.3.1 (2015-08-19)

• 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

circlize 0.3.0 (2015-08-01)

• '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.

circlize 0.2.5 (2015-07-08)

• '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'

circlize 0.2.4 (2015-03-20)

• '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)

circlize 0.2.3 (2015-02-22)

• 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()'

circlize 0.2.2 (2015-01-30)

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

circlize 0.2.1 (2015-01-09)

• 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', ...

circlize 0.2.0 (2014-12-08)

• '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'

circlize 0.1.3 (2014-11-07)

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

circlize 0.1.2 (2014-10-13)

• 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

circlize 0.1.1 (2014-09-01)

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

circlize 0.1.0 (2014-08-02)

• 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

circlize 0.0.9 (2014-07-11)

• 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 https://jokergoo.github.io/circlize
• re-implement 'colorRamp2'

circlize 0.0.8 (2014-06-03)

• 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'

circlize 0.0.7 (2013-10-01)

• add an example in demo codes
• improved vignettes

circlize 0.0.6 (2013-09-02)

• 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

circlize 0.0.5 (2013-08-03)

• 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.

circlize 0.0.4 (2013-07-05)

• 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

circlize 0.0.3 (2013-06-02)

• 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'

circlize 0.0.2 (2013-05-26)

• 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