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
