486 lines
22 KiB
Plaintext
486 lines
22 KiB
Plaintext
Changes in version 0.4.15
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-----------------------------------------------------------------------
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* low-level graphics functions won't change the index of sector and track.
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* `colorRamp2()`: add `hcl_palette` argument.
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* `highlight.sectors()`: argument `padding` supports to wrap the vector with `I()`.
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* fixed a bug of wrong calculation of label positions in `circos.genomicLabels()`.
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Changes in version 0.4.14
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-----------------------------------------------------------------------
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* `circos.genomicTrackPlotRegion()`: add `na.rm = TRUE` when using `range()`.
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* fixed a bug of `na.col` in `circos.heatmap()`.
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* improved default order of link end when duplicated rows exist in the data frame.
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* `circos.heatmap()`: add `cell.border`, `cell.lty` and `cell.lwd` arguments.
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* add `circos.initializeCircularGenome()`.
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* `chordDiagram()`: `link.sort` allows to sort links based on the original orders
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in the input data frame.
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* label facing is correct now for y-axis when circos.par$xaxis.clock.wise is FALSE.
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* `rand_color()`: add a new argument `friendly` that generate eye-friendly random colors.
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* `chordDiagram()`: fixed a bug when a sector have all zero values and after scaling
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they changed to NA.
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Changes in version 0.4.13
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-----------------------------------------------------------------------
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* `circos.link()`: add offset when testing whether the link is out of the sector.
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Changes in version 0.4.12
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-----------------------------------------------------------------------
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* `smartAlign()`: improved boxes overlapping
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* `circos.heatmap()`: automatically convert the input to a matrix if
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it is a data frame
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* now validate the regions to check whether the regions are exceeding
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the chromosomes.
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* `circos.link()`: add a new `inverse` argument to control whether the link
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is inversed or not.
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* `circos.genomicLabels()`: replace `side` argument with `labels.side`.
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* `circos.points()`, `circos.lines()`, `circos.text()` allow argument `x` to be
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a two-column matrix.
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* add `arrange_links_evenly()` function.
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* add `circos.connect()` function.
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* `circos.heatmap()`: argument `cluster` can be a clustering object.
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* `circos.heatmap()`: add `cell_width` to control the relative width of heatmap cells.
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* add `circos.labels()`.
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* `chordDiagram()`: bars are drawn according to the visibility of links.
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Changes in version 0.4.11
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-----------------------------------------------------------------------
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* `chordDiagram()`: add `link.auto` argument
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* `chordDiagram()`: add `link.target.prop` and `target.prop.height` arguments
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* `circos.par()`: add `circle.margin` option
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* `circos.genomicLabels()`: fixed a bug when `direction = "outside"`
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* add `xaxis.clock.wise` option in `circos.par()`
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* `chordDiagram()`: now the scaling is properly applied.
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* `chordDiagram()`: link positions are optimized so they have minimal intersections.
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`link.auto` argument is ignored and removed.
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* `circos.dendrogram()`: support arbitary numbers of branches on each node.
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* all functions with `factors` with arguments change to `sectors`.
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Changes in version 0.4.10
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-----------------------------------------------------------------------
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* `highlight.sector()`: fixed a bug when circos.par("clock.wise" = FALSE)
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* `circos.genomicLink()`: input data frames can have 2 columns. In this case
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the start and the end positions of each region are the same.
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* `circos.circos.trackPlotRegion()`: fixed a bug that sector index was wrongly
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assigned.
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* `get.cell.meta.data()`: add `cell.width` and `cell.height` arguments.
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* `circos.genomicTrackPlotRegion()`: when input is a data frame list and column.index
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is a vector, reduce the one-column data frame to a vector.
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* add `add.track.meta.data()` and `add.sector.meta.data()` too add user-defined cell meta data.
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* add `circos.heatmap()` to draw multi-track heatmaps.
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* add `circos.barplot()`, `circos.boxplot()` and `circos.violin()`.
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* sector index are all enforced to be character.
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* `circos.nested()`: now the graphic parameters are reordered accordingly as the `correspondance`.
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* add `mm_x()`, `mm_y()`, `mm_h()`, `cm_x()`, `cm_y()`, `cm_h()`, `inches_x()`, `inches_y()`, `inches_h()`
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functions
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* `circos.initialize():` if `gap.degree`/`gap.after` is set a named vector, the order of
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these two options are adjusted to the real sector order.
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* add `set_track_gap()` function.
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* `circos.link()`: add `reduce_to_mid_line` argument.
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* `chordDiagram()`: add `group` argument.
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Changes in version 0.4.9
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-----------------------------------------------------------------------
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* `chordDiagram()`: fixed a bug when `link.overlap = TRUE` for sparse matrices.
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* `circos.rect()`: add `rot` argument.
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* add `circos.triangle()`.
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* all examples are included in R source code files
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* `circos.genomicHeatmap()`: `connection_height` can be set to `NULL` to remove the
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connection lines.
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* `genomicDensity()`/`circos.genomicDensity()`: add a new `count_by` argument so that
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the overlap can be calculated as how many regions overlap to the windows.
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* `circos.trackPlotRegion()`: cells in all sectors are plotted if `fa` does not provide complete
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set of categories.
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* `circos.initialize()`: give warnings if `fa` is in numeric mode.
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* `circos.track()`/`circos.genomicTrack()`: gives error when the panel function was specified without
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explicitly by the name `panel.fun`.
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* `chordDiagram()`: if the input is a data frame, it allows the data frame to have two numeric columns
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and the link ends are drawn wiht unequal width.
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Changes in version 0.4.8
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-----------------------------------------------------------------------
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* add `validate_regions()` to check the end positions and start positions.
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* `colorRamp2()`: fixed a bug when the color mapping function returns RGB matrix.
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* `circos.genomicHeatmap()`: add `na_col` argument.
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* `chordDiagram()`: add `link.overlap` argument.
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Changes in version 0.4.7
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-----------------------------------------------------------------------
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* fixed a bug that the vertical line was wrongly put for `circos.yaxis()`.
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* validate input if it is should be a data frame.
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* `colorRamp2()`: add HLS colorspace
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* add `major.at` and `labels` arguments to `circos.genomicAxis()`.
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* circos.initializeWithIdeogram(): manually select chromosomes for the common species
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* `chordDiagram()`: fixed a bug that after reducing the matrix/data frame
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by `reduce`, there might be sectors with zero width.
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* optimized `circos.nested()`
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* `colorRamp2()`: check NA values
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Changes in version 0.4.6
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------------------------------------------------------------------------
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* smartAlign(): the order of values won't affect the realignment now.
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* `circos.rect()`, `circos.segments()`, `circos.points()`, `circos.text()`:
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x and y are recycled if the length of the variable is 1.
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* fixed a bug of the position of vertical line in `circos.yaxis()`
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* add `facing` and `niceFacing` to `circos.genomicLabels()`
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* `posTransform.text()`: linking lines will not be overlapping anymore.
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Changes in version 0.4.5
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------------------------------------------------------------------------
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* vertical lines added for y-axis.
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* add `axis.labels.cex` and `labels.cex` in `circos.genomicInitialize()`.
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* remove `lwd` in `circos.genomicRect()` because `lwd` is not allowed to be vector.
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* fixed a bug when self.link = 1 in chordDiagram()
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* add `scale` in chordDiagram()
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* `circos.initialize()`: convert xlim and x to numeric
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* `colorRamp2()` is faster now.
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* add `circos.genomicAxis()`.
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* add `calc_gap()`.
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* `chordDiagram()`: consider tibble format as input.
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Changes in version 0.4.4
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-------------------------------------------------------------------------
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* update denpendency of GlobalOptions package
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* `genomicDensity()`: add `chr.len` argument.
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Changes in version 0.4.3
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--------------------------------------------------------------------------
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* `circos.trackHist()`: add `area` argument to add filled color under density lines.
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* `getColorInfo()`: use `ls(envir)` to get the names of variables in the environment.
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* `circos.arrows`: add instructions of making reverse clockwise arrows.
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Changes in version 0.4.2
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---------------------------------------------------------------------------
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* add startup message
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* add `xmax` argument in `chordDiagram()`
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* first column is refactorized in `circos.initialize()`
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* add names for CELL_META
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* add `labels.pos.adjust` in `circos.axis()`
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* add `fontsize()` function
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* `circos.nested()`: check whether sector order in the two circular plots are consistent
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* `getQuadraticPoints()`: add tiny offset when the curve is actually a straight line
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Changes in version 0.4.1
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---------------------------------------------------------------------------
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* add `circos.raster()`
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* add `circos.arrow()`
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* re-implement `rand_color()`
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* support `col` in `circos.axis()`
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* `circos.genomicLabels()`: regions are automatically sorted in advance
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Changes in version 0.4.0
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----------------------------------------------------------------------------
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* add `link.visible` argument in `chordDiagram()`
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* add cytoband files and chromInfo files for a list of species locally
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* add a new vignette "Add legends to circlize"
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* add a new function `convert_*()` which convert an absolute unit to
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measurement in different coordinates
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* enforce asp = 1 when calling plot.default
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* length of axes ticks are set to 2mm by default
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* in axis, the first axis label is shifted if it is exceed the axis and
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so is for the last axis label.
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* text.vjust accepts strings as "2mm", "-2.1 cm" to represent offsets
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* `circos.segments()`: graphic parameters can be set as vectors
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* add `circos.genomicIdeogram()`, `circos.genomicHeatmap()`, `circos.genomicLabels()`
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* add `circos.nestes()`
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* vignette has been moved to https://jokergoo.github.io/circlize_book/book/index.html
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* add `set.current.cell()`
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* add `h.ratio` argument in `circos.link()`
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Changes in version 0.3.10
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----------------------------------------------------------------------------
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* `chordDiagram()`: fixed a bug when the input matrix is stored as a data frame
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* `rainfallTransform()`: add "left" and "right" modes, and now the row order of
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the output data frame is as same as the input one.
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* `circos.genomicInitialize()`: it can only plot axes now.
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* `posTransform.text()`: add `extend` option to control the extension of chromsomes
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to allow to put more labels
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* `ciros.points()`: add `bg` option to control background color
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Changes in version 0.3.9
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----------------------------------------------------------------------------
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* `chordDiagramFromDataFrame()`: now recognize a `rank` column which defines
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the order of adding links
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Changes in version 0.3.8
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----------------------------------------------------------------------------
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* chordDiagram(): if not all sectors are specified in grid.col, remaining will
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be filled by random colors
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* if `ylim` has same values for upper and lower bound, throw errors.
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Changes in version 0.3.7
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----------------------------------------------------------------------------
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* chordDiagram() now returns a data frame which contains positions of all links
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* chordDiagram() track.margin is also taken into settings of preAllocateTracks
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* chordDiagram(): link.sort adds a new option: "overall" which sort links
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regardless of rows or columns
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* chordDiagram(): add `link.largest.ontop` which controls the order of adding links
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Changes in version 0.3.6
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----------------------------------------------------------------------------
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* positions of arrows in chordDiagram() have been adjusted.
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* fixed a bug that negative value was not shown
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* circos.initialize: if `factors` are unique and is a vector, the order of sectors
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will be the same as `factors`.
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* `highlight.sector`: text are now in correct position if sectors are over theta = 0
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Changes in version 0.3.5
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----------------------------------------------------------------------------
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* `chordDiagram()`: if the corresponding value is zero, nothing happens.
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* border of links are same as filled by default
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* explicitely put all arguments in `chordDiagram()` instead of just using `...`
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* `adj` in `circos.text()` can also adjust text rotations.
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* 'circos.genomicInitialize()': gap between labels and ideograms is adjusted
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if there is no axis
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Changes in version 0.3.4
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----------------------------------------------------------------------------
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* `circos.genomicLink()`: ordering is cancled when normalizing the data frames
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* export `smartAlign()`
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Changes in version 0.3.3
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----------------------------------------------------------------------------
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* `rainfallTransform()` and `genomicDensity()`: can be applied on the bed-format
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data frame directly.
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* add `col2rgb()` which transforms back to the original value based on the color
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mapping function.
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* add `circos.yaxis()`
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Changes in version 0.3.2
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-----------------------------------------------------------------------------
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* `chrodDiagram`: add warning if users use data frame as ajacency matrix
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* `circos.genomicTrackPlotRegion`: data frame will be sorted
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Changes in version 0.3.1
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-----------------------------------------------------------------------------
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* fixed a bug for `chordDiagramFromDataFrame` when there is the third column in the data frame
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* `colorRamp2`: colors are interpolated linearly in Lab color space
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* `chordDiagram`: directional, direction.type and diffHeight can also be vector
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Changes in version 0.3.0
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-----------------------------------------------------------------------------
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* `chordDiagramFromMatrix`: automatically replace NA to 0 in the input matrix
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* add `chordDiagramFromMatrix` and `chordDiagramFromDataFrame`
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* by default there is axis on chord diagram
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* add `quadratic.bezier.length` that calculates the approximate length of bezier curve
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* normalize link-related functions to make sure the direction is always from
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the first argument to the second argument, reverse clockwise.
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Changes in version 0.2.5
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-----------------------------------------------------------------------------
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* `circos.rect` and `circos.polygon` are vectorized
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* `circos.dendrogram`: supports graphical settings for nodes
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* `circos.link`: support 'big.arrow' mode for links
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* `circos.text`: graphical settings are subsetted correctly in `niceFacing` is set
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* add shortcut functions: `circos.track`, `circos.update` and `circos.genomicTrack`
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* add `normalizeChordDiagramGap`
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* fixed type in `get.cell.meta.data`
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Changes in version 0.2.4
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------------------------------------------------------------------------------
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* 'chrodDiagram`: If graphic parameters for links are different, the value can be
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specified as a three-column data frame.
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* `chordDiagram`: arrows can be used to identify directions
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* ·circos.link`: arrows can be used to identify directions
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* `chordDiagram`: width of self-links are not duplicated.
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* `circos.link`: if two roots for a link overlaps, the link is de-generated
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as an area with a quadratic curve and an arc.
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* add `circos.dendrogram` which draw dendrograms (dendrogram can be rendered by
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`dendextend` package)
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Changes in version 0.2.3
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------------------------------------------------------------------------------
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* add `link.order` argument in `chordDiagram` to control order of links on
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sectors
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* add `highlight.sector`
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* `chromosome.index` can set the order of chromosomes
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* add `read.chromInfo()` to read chromInfo file from UCSC
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* if downloading cytoband file failed, try to download chromInfo file
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* `chromosome.index` can be set in `read.cytoband()` and `read.chromInfo()`
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Changes in version 0.2.2
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------------------------------------------------------------------------------
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* change `.onLoad` to `setLoadActions`
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* `circos.clear`: __tempdir__ will not be reset
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Changes in version 0.2.1
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------------------------------------------------------------------------------
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* If par("mar") is using default, it will be changed to par(mar = c(1, 1, 1, 1))
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internally and will be recovered after calling circos.clear()
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* `circos.text`: add two options ('bending.inside' which is identical to original
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'bending' and 'bending.outside'), both support `niceFacing`
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* circos.par('__tempdir__') is initialized by `tempdir()`
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* `.get_color`: there will be no negative value due to 0.000 - 0.000
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* `chordDiagram`: `grid.col` is correctly reduced if rownames and colnames overlap
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* `circos.text`: `font` is passed to `text` function
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* `colorRamp2`: returned function has an attribute: `breaks`
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* `chordDiagram`: assign same names for rows and columns if the input matrix
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is specified symmetric while has no names
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* `chordDiagram`: also check rownames and colnames if the matrix is specified as
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symmetric.
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* don't remove temporary folder
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* `value` can be scalar or vector in `circos.genomicPoints`, `circos.genomicLines`, ...
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Changes in version 0.2.0
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------------------------------------------------------------------------------
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* `draw.sector` is modified, now accepts an argument `clock.wise` to control
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the direction of sectors.
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* `highlight.chromosome` can highlight more than one chromosomes now.
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* vignettes are rendered by `knitr`
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* set default transparency to 0.5 in `chordDiagram`
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* `circlize` returns value when track.index == 0
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* fixed a bug when text facing is 'bending', all text are plotted in one cell
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* different colors for each rows can be set to `circos.genomicLines` if
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type %in% c("segment", "h")
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* pre-allocate the matrix in `.get_color`
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Changes in version 0.1.3
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------------------------------------------------------------------------------
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* add `jitter` for adding points under `stack` mode
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* value in `panel.fun` can be selected by character index
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* change default temporary dir to `tempdir()`
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Changes in version 0.1.3
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------------------------------------------------------------------------------
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* temporary add dependency of `methods` until bugs in `GlobalOptions` fixed
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* add `reduce` argument in `chordDiagram` to control whether to remove tiny categories
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* add `species` argument in `generateRandomBed`
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* change use of posTransform.text
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* add names for `chr.len` in `read.cytoband`
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* cytoband files are cached
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* `row.col`, `column.col`, `col`, `grid.col` and circos.par('gap.degree') will
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also be reduced if the matrix is reduced
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Changes in version 0.1.2
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------------------------------------------------------------------------------
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* global options are controlled by `GlobalOptions` package
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* set `par("lend")` and `par("ljoin")` to their default values.
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* add more example codes in genomic_plot vignette
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Changes in version 0.1.1
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------------------------------------------------------------------------------
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* fixed the bug that if start position is not zero when calling `circos.genomicIntialize`,
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``major.at`` is wrongly calculated.
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Changes in version 0.1.0
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------------------------------------------------------------------------------
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* height(h) and shape(w) can be set for Bezier curve (in `circos.link`)
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* add examples in man/
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* add ``fromRows`` options in `chordDiagram` to control the direction of links
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* Now the ``major.by`` are the same in all sectors
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* define ``min.data`` and ``max.data`` in internal variable ``SECTOR.DATA``
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* check that sector names cannot be empty strings ("")
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* check whether circos plot has been initialized when calling `circos.trackPlotRegion`
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* add ``niceFacing`` in `circos.text` to make the facing more human easy
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* height of ideogram and annotation track in `circos.initializeWithIdeogram` and `circos.genomicInitialize` can be set
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* some example code in examples/vignettes has been changed according to changes in the package source code
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* add `posTransform.text` which can smartly put text on the circle
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* ``track.margin`` and ``cell.padding`` can be set in `circos.trackPlotRegion` as a local setting
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Changes in version 0.0.9
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------------------------------------------------------------------------------
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* links are now implemented by Bezier curve
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* baseline can be set when ``type == "h"`` `in circos.lines`
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* add a new function `chordDiagram` which support chord diagram
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* add `facing` argument to replace `direction` in `circos.text`
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* `circos.trackPlotRegion` can be used to update a track without re-setting ylim
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* move demo to https://jokergoo.github.io/circlize
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* re-implement `colorRamp2`
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Changes in version 0.0.8
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------------------------------------------------------------------------------
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* axes labels will not draw when setting labels = FALSE
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* add many functions supporting genomic visualization
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* add a new vignette to show how to plot genomic circos plot with new functions
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* add `circos.info`
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Changes in version 0.0.7
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------------------------------------------------------------------------------
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* add an example in demo codes
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* improved vignettes
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Change in version 0.0.6
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* order will not change in `circos.trackPlotRegion` when not specifying `factors`, bug fixed
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* add an example in 'draw relation' vignette
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* add a new vignette focusing on phylogenetic tree
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* support directly downloading cytoBand file from UCSC
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Changes in version 0.0.5
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* support self-define width of sectors when initializing sectors
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* add simple functions to read and manuplate cytoband file
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* add several new figures in the vignettes and vignettes have been improved.
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* ``cell.padding`` in `circos.par` now using degree as its measurement.
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* ``track.margin`` in `circos.par` now using percentage of radius as its measurement.
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Changes in version 0.0.4
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* number of points to simulate quadratic curves decreased
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* labels on axis in `circos.initializeWithIdeogram` is now 'vertical_right' by default
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* size of the vignettes reduced
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* add example of drawing heatmap and cluster dendrogram in the main vignette
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* add example of drawing error area of lines by `circos.polygon`
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* vignette improved
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* ``gap.degree`` in `circos.par` can be a vector which means different degrees for gaps can be set
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* export core function `circlize` now
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* track.margin now is in correct order
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* links are optimized (although not so perfect)
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* no point overflow warnings when drawing axes
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Changes in version 0.0.3
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* vignettes has been improved
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* ``xplot`` in `get.cell.meta.data` is now corresponding to the data direction in the cell
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* number of points to draw links decreased.
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* `get.cell.meta.data` can provide more meta data for a cell
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* start degree and end degree now consistent with the data axis.
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* the first sector is drawn first now.
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* add `draw.sector`
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Changes in version 0.0.2
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* add `draw.sector` so it would be more straightforward to highlight sectors
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* add ``track.margin``, ``cell.padding``, ``cell.xlim`` and ``cell.ylim`` in `get.cell.meta.data` function
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* figures in vignettes are all generated automatically
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* vignettes have been imporved
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