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Changes in version 0.3.11
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* 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"
Changes in version 0.3.10
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* `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
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* `chordDiagramFromDataFrame()`: now recognize a `rank` column which defines
the order of adding links
Changes in version 0.3.8
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* 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
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* 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
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* 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
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* `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
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* `circos.genomicLink()`: ordering is cancled when normalizing the data frames
* export `smartAlign()`
Changes in version 0.3.3
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* `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
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* `chrodDiagram`: add warning if users use data frame as ajacency matrix
* `circos.genomicTrackPlotRegion`: data frame will be sorted
Changes in version 0.3.1
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* 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
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* `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
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* `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
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* '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
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* 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
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* change `.onLoad` to `setLoadActions`
* `circos.clear`: __tempdir__ will not be reset
Changes in version 0.2.1
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* 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
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* `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
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* 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
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* 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
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* 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
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* 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
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* 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
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* 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
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* 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
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* add an example in demo codes
* improved vignettes
Change in version 0.0.6
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* 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
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* 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
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* 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
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* 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
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* 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