-
Notifications
You must be signed in to change notification settings - Fork 41
/
NEWS
178 lines (104 loc) · 5.35 KB
/
NEWS
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
Changes in version 1.21.0
-------------------------
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
BUG-FIXES
o Fixed wrong positioning of chromosome names in some edge cases (github issue 114)
o kpAddLabels now work on zoomed in regions (github issue 112)
Changes in version 1.10.0
-------------------------
NEW FEATURES
SIGNIFICANT USER-VISIBLE CHANGES
BUG-FIXES
o kpPlotGenes and kpPlotTranscripts no longer flip strands when plotting on
data.panel=2
o kpPlotRainfall does not error when a chromosome has no data
o Fixed inversion bug in plot.type=5
Changes in version 1.10.0
-------------------------
NEW FEATURES
o Added new color managements functions including is.color and transparent
and improved the existing ones.
o Added new functions to color data elements based on different features:
chromosome, position, overlapping of regions...
o Improved gene and transcript plotting functions. Added functions to
automatically get gene symbols from OrgDb objects. Improved transcript
and gene positioning. Added a function to merge all transcripts of a gene
into one.
o kpPlotBigWig can now adjust the ymax value based on the global maximum,
per chromosome or taking into account only the visible region.
SIGNIFICANT USER-VISIBLE CHANGES
o It is now posible to add labels to the right-hand side of chromosomes
with kpAddLabels
o Improved documentation and vignette
o makeGenesDataFromTxDb does not need a karyoplot anymore. Changed parameter
order.
BUG-FIXES
o It is now possible to use cex in plotKaryotype to specify chromosome name sizes
o Multiple small bug fixes
Changes in version 1.7.17
-------------------------
NEW FEATURES
o Added autotrack function to automatically assign r0 and r1 values
o Added kpAddChromosomeSeparators to draw lines between chromosomes
o Added new plot types: "ideogram" to plot on the ideogram itself and "all" to plot over all data.panels and the ideogram
o Added kpPlotBigWig to plot data on BigWig files
o Added regioneR::toGRanges to plotKaryotype zoom, so it's now possible to specify a zoom region with UCSC style region definition (i.e. "chr2:232122-321123")
o Added colByChr function to assign colors to data elements depending on their chromosome
SIGNIFICANT USER-VISIBLE CHANGES
o Added internal conversion to GenomicRanges using regioneR::toGRanges to kpPlotRegions. It is now possible to directly plot the regions in a BED file, for example.
BUG FIXES
o Fixed a bug in the coordinate change function where plotting was out of place
o Fixed a bug in kpPlotCoverage where the coverage would not extend to the end of the chromosome
o Several minor bug fixes
Changes in version 1.7.9
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o New parameter in kpPlotMarkers to allow labels to move beyond the
chromosome limits when repositioning to avoid label overlaps
BUG FIXES
o Fixed a bug in the coordinate change function where plotting was out of place
or even invisible if the zoom object had addition seqlevels
Changes in version 1.7.4
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o The zoom region in plotKaryotype can be specified in any format accepted
by regioneR::toGRanges, including UCSC/IGV style "chr9:23000-40000".
Changes in version 1.7.3
-------------------------
NEW FEATURES
o Added `kpPlotBAMCoverage` to plot the exact coverage from a BAM file
SIGNIFICANT USER-VISIBLE CHANGES
o Improved performance of kpPlotBAMDensity. Specially in zoomed plots.
BUG FIXES
o kpAxis: Axis were not visible in zoomed plots. They are now visible.
Changes in version 1.7.1
-------------------------
NEW FEATURES
o Added `kpPlotBigWig` to plot data in bigwig files, usually data derived from BAM coverage for ChIP-seq, etc...
SIGNIFICANT USER-VISIBLE CHANGES
o Added a `digits` parameter to `kpAddBAseNumbers` to control the number of digits after the decimal point in genome position lables
Changes in version 1.5.4
NEW FEATURES
o Added `kpPlotGenes` and `kpPlotTranscripts` to plot gene and transcript models
o Added `kpArea` to plot shaded areas. Ideal for coverage plots, RNA-seq, ChIP-seq, etc...
SIGNIFICANT USER-VISIBLE CHANGES
o Added plot.type=4 to `plotDefaultPlotParams`
o Added new examples and extended the tutorial at the karyoploteR tutorial and examples site at https://bernatgel.github.io/karyoploter_tutorial/
BUG FIXES
o Various minor bug fixes.
o Various documentation fixes
Changes in version 1.3.11
NEW FEATURES
o Added zooming to create plots of regions smaller than a whole chromosome.
o Added `kpPlotLoess` to plot a fitted loess and confidence interval for data points.
o Added `kpPlotRainfall` to create rainfall plots from variants.
o Added `kpPlotLinks` to plot connections between genome regions even in different chromosomes.
SIGNIFICANT USER-VISIBLE CHANGES
o New default in `plotKaryotype`: now `plot.type` defaults to 1, a ideogram with a single data panel above it
## Other
o Added unit testing
o Created a karyoploteR tutorial and examples site at https://bernatgel.github.io/karyoploter_tutorial/
BUG FIXES
o Fixed a bug causing a misalignment between data points and plotting parameters in some edge cases.
o Various minor bug fixes.