File: NEWS

package info (click to toggle)
r-cran-circlize 0.4.5-1
  • links: PTS, VCS
  • area: main
  • in suites: buster
  • size: 3,312 kB
  • sloc: makefile: 8
file content (355 lines) | stat: -rwxr-xr-x 16,418 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
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