/usr/lib/R/site-library/Gviz/NEWS is in r-bioc-gviz 1.22.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | CHANGES IN VERSION 1.20.0
-------------------------
BUG FIXES
o BiomartGeneRegionTracks can now deal with a featureMap list to provide
alternative conditional mappings for different Biomarts.
CHANGES IN VERSION 1.18.0
-------------------------
BUG FIXES
o Various bug fixes.
CHANGES IN VERSION 1.16.0
-------------------------
NEW FEATURES
o AlignmentsTracks will nor use the transformation display
parameter to adjust the plotting of the coverage.
CHANGES IN VERSION 1.11.0
-------------------------
NEW FEATURES
o BiomartGeneRegionTracks can now be created based on a gene
symbol, Ensembl trancript id, Ensebml gene id or ENTREZ gene id.
SIGNIFICANT USER-VISIBLE CHANGES
o Streaming behaviour for BiomartGeneRegionTracks. Already queried
regions are cached, and new data is fetched from Biomart on
demand.
o Proper handling of UCSC genome identifiers in
BiomartGeneRegionTracks. Automated mapping to Ensembl genome
versions and Biomart archives.
BUG FIXES
o A number of significant fixes.
CHANGES IN VERSION 1.10.0
-------------------------
BUG FIXES
o Various bug fixes.
CHANGES IN VERSION 1.9.0
-------------------------
NEW FEATURES
o The new CustomTrack class to allow for user-defined plotting functions.
SIGNIFICANT USER-VISIBLE CHANGES
o The collapseTranscripts parameter now offers more control over the type of collapsing.
CHANGES IN VERSION 1.8.0
-------------------------
NEW FEATURES
o The new HighlightTrack class to add a comon highlighting region
for multiple tracks.
o The new OverlayTrack class to merge the panels of multiple
tracks into a single panel.
o The reverseStrand display parameter lets you plot the data
relative to the negative strand.
o The just.label display parameter adds control to the placement
of group labls in AnnotationTrack and GeneRegionTrack objects.
o The box.legend display parameter to add a box around the legend
in a DataTrack object.
o extend.right and extend.left now also take relative expansion
factors (as values between -1 and 1).
o A new shape type fixedArrow for AnnotationTrack and
GeneRegionTrack objects, and the arrowHeadWidth and
arrowHeadMaxWidth parameters to better control the arrow shapes.
o Display parameter schemes to persistently modify parameter
settings.
o The new featureAnnotation and groupAnnotation parameters to
better control the feature and group labels in AnnotationTracks.
o The new exonAnnotation and transcriptAnnotation parameters to
better control the exon and transcript labels in
GeneRegionTracks.
o The new AlignmentsTrack class to visualized aligned NGS reads in
a BAM file.
BUG FIXES
o A number of significant fixes.
SIGNIFICANT USER-VISIBLE CHANGES
o Some display parameter names have been reworked, but the old
ones should still work as aliases.
o Overplotting in AnnotationTrack and GeneRegionTrack objects has
been minimized to be able to make better use of alpha
blending. Also the way composite exons (e.g. part UTR, part CDS)
are plotted has been changed. Those will now be merged into one
feature as long as the exon identifier is identical and if they
can be reduced into a single range wit min.gapwidth=1.
CHANGES IN VERSION 1.6.0
-------------------------
NEW FEATURES
o The DataTrack class now comes with a new horizon plot type
thanks to input from Ge Tan.
SIGNIFICANT USER-VISIBLE CHANGES
o isActiveSeq and isActiveSeq<- are deprecated in GenomicFeatures
and their methods have been removed from Gviz.
CHANGES IN VERSION 1.4.0
-------------------------
NEW FEATURES
o BiomartGeneRegionTracks will now make use of the available CDS
information in Ensembl.
o The constructors to the AnnotationTrack, GeneRegionTrack,
DataTrack and SequenceTrack classes now accept a character
scalar that points to a file on the file system. A number of
default parser functions have been implemented to read the
standard file types. Alternatively, a user-defined import
function can be provided. This feature also supports streaming
from indexed file types like BAM or bigWig, in which case the
data is fetched dynamically upon each plotting operation.
o The mart object in BiomartGeneRegionTrack objects is now cached
in order to speed up subsequent queries to the same mart.
o When plotting DataTracks with type 'gradient' or 'heatmap', a
color scale is plotted next to the regular y-axis to indicate
the mapping of numeric values in the false color range. Thanks
to Mark Heron for his code contribution.
o Sample names can now be shown in heatmap-type plots by setting
the 'showSampleNames' display parameter.
SIGNIFICANT USER-VISIBLE CHANGES
o Complete refactoring of the automatic font size adjustments to
provide more reasonable defaults.
o Tick labels on the genomic axis are now show in between tick
marks when zoomed in to single nucleotide level.
BUG FIXES
o Fixed a bug in IdeogramTracks where all bands in the rounded
caps at the edges of the Ideogram were missing.
o The way genomic ranges are plotted is now according to the Lego
block model suggested by Herve. This is only relevant when zooming
in to the level of single nucleotides.
o Tick labels on the genome axis show only significant digits now.
o Sample ordering in heatmap plots is now correct.
o Numerous little fixes.
CHANGES IN VERSION 1.2.0
-------------------------
NEW FEATURES
o A SequenceTrack class has been added to draw genomic sequence
information on a Gviz plot. Possible inputs for the track are
DNAStringSet objects or directly from BSgenome packages.
o GeneRegionTracks can now deal with coding and non-coding regions
by means of the feature property in combination with the
thinBoxFeature display parameter.
o StackedTracks now have a new display parameter 'reverseStacking'
which reverts the horizontal ordering of stacked items. If set
to TRUE, the lowest items are moved to the top of the stack, and
vice versa.
SIGNIFICANT USER-VISIBLE CHANGES
o Updated the show methods for most tracks to give more meaningful
and more compact information about the track's
content. Availablability of data on other chromosomes than the
currently active one should now be indicated.
o IdeogramTracks can now be constructed from a cytoband table via
the new bands argument in the constructor.
o AnnotationTrack objects now by default draw connecting lines in
a light gray color. This feature can be controlled via the
col.line display parameter.
o Sliding window summarization can now deal with NA values.
o Exporting drawGD from the name space now to allow for
sub-classing of GdObjects in other packages.
o When building GeneRegionTracks from TranscriptDb objects the
information about UTRs and coding regions is now retained.
BUG FIXES
o When zooming into the emty space between two grouped features,
the connecting line will now be plotted for all classes inheriting
from AnnotationTrack.
o An error in calculating ylims when drawing AlignedReadTracks has
been fixed.
o Numerous other little fixes that mainly aim at improving
performance.
|