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NEWS
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Changes in version 1.43.5
o Update email address.
Changes in version 1.43.5
o Add line and histogram to tracktype for trackstlye.
Changes in version 1.43.4
o Remove the clip for annotation track.
Changes in version 1.43.3
o Add documentation to remove y label.
Changes in version 1.43.2
o Make it possible to plot annotation for peak regions.
Changes in version 1.43.1
o Make it possible to plot link for back2back interaction data.
Changes in version 1.41.10
o Improve the plot speed for interaction data.
Changes in version 1.41.9
o Add a simple gene track plot model.
Changes in version 1.41.8
o Add listNormalizations function.
Changes in version 1.41.7
o Fix the bug that newpage parameter not used for plotGRanges.
Changes in version 1.41.6
o Add `legendPosition` parameter for lollipop plot.
Changes in version 1.41.5
o Export the method `$` for trackStyle class.
Changes in version 1.41.4
o Move the 3d plots to a different package.
Changes in version 1.41.3
o plot lolliplot with multiple shapes in one position.
Changes in version 1.41.2
o export view3dStructure function.
Changes in version 1.41.1
o Add mdsPlot function.
Changes in version 1.39.17
o Fix the legend with alpha for lolliplot.
Changes in version 1.39.16
o Import txdbmaker.
Changes in version 1.39.15
o Optimize the reduce function for loopBouquetPlot.
Changes in version 1.39.14
o reduce the input for loopBouquetPlot.
Changes in version 1.39.13
o Handle the empty input for loopBouquetPlot.
Changes in version 1.39.12
o Update the safe text algorithm for loopBouquetPlot.
Changes in version 1.39.11
o Add parameter safe_text_force for loopBouquetPlot.
Changes in version 1.39.10
o Add color for geneTrack.
Changes in version 1.39.9
o Fix multiple bugs in loopBouquetPlot.
Changes in version 1.39.8
o Change loopBouquetPlot to grid plot.
Changes in version 1.39.7
o Fix the example for loopBouquetPlot.
Changes in version 1.39.6
o add loopBouquetPlot.
Changes in version 1.39.5
o Browse heatmap by js (scratch).
Changes in version 1.39.4
o Fix the issue if the first label is empty for lolliplot.
Changes in version 1.39.3
o Fix the mismatch data track when change the ylim in browseTracks.
Changes in version 1.39.2
o Fix the wrong plot for multiple genes track in browseTracks.
Changes in version 1.39.1
o Fix the y-axis for lollipop plot.
Changes in version 1.37.15
o Fix reading valid pairs typo.
Changes in version 1.37.14
o update the lollipopPlot documentation to fix the issue
unable to find an inherited method for function 'content' for
signature 'response'.
Changes in version 1.37.13
o fix the feature legend space.
Changes in version 1.37.12
o add ARA function.
o fix the missleading color legend of interaction data.
o fix the bug in addInteractionAnnotation.
Changes in version 1.37.11
o fix the minimal font of optimized style.
Changes in version 1.37.10
o add function GIoperator.
Changes in version 1.37.9
o add function addInteractionAnnotation for Interaction data.
Changes in version 1.37.8
o change the filter condiction for tads annotation of Interaction data.
Changes in version 1.37.7
o add tads annotation for Interaction data.
Changes in version 1.37.6
o add lollipop_style_switch_limit for lollipop plot.
Changes in version 1.37.5
o add border_color for Interaction data.
Changes in version 1.37.4
o update the documentation for lollipopPlot for changes of the snp label.
Changes in version 1.37.3
o use strawr to replace the local C++ script.
Changes in version 1.37.2
o remove the CXX_STD = CXX11 from straw Makevars.
Changes in version 1.37.1
o add stop message when there is negative values for grid.pie plot.
Changes in version 1.35.5
o use straw for hic import.
Changes in version 1.35.4
o handel label.parameter.draw for labels.
Changes in version 1.35.3
o Add documentation for selected labels for mutations.
Changes in version 1.35.2
o Add support for node label parameters.
Changes in version 1.35.1
o Add support for single resolution cooler file.
Changes in version 1.33.8
o Fix a bug if there is no name for the freatures.
Changes in version 1.33.7
o print the more pseudocode in browseTracks.
Changes in version 1.33.6
o Fix the bug for 'invalid color name' in browseTracks
o print the pseudocode in browseTracks
Changes in version 1.33.5
o Change the cool file open flag to "H5F_ACC_RDONLY"
Changes in version 1.33.4
o Fix a issue for plot tracks by insert 0 to the first signals.
Changes in version 1.33.3
o Add support for motif logo for lollipop plot.
Changes in version 1.33.2
o Add support for multiple operators for viewTrack.
Changes in version 1.33.1
o Fix the bug when locateScale return NA values.
Changes in version 1.31.4
o Fix the issue in windows 2022.
Changes in version 1.31.2
o Handle the issue with long tail.
Changes in version 1.31.1
o Move the heatmap legend to yaxis.
Changes in version 1.29.8
o Fix the a typo in read hic data.
Changes in version 1.29.7
o Fix the bug 'breaks' are not unique
Changes in version 1.29.6
o Add smooth curve to the tracks.
Changes in version 1.29.5
o Improve gene track plots.
Changes in version 1.29.4
o Fix the issue for auto-rescale lolliplot by emphasizing exon region
when there are continues exons.
Changes in version 1.29.3
o Add the possibility to lolliplot to emphasize exon or intron region.
Changes in version 1.29.2
o Fix the yaxis when user supplied yaxis is greater than max scores.
Changes in version 1.29.1
o Update documentation lolliplot for rescale parameter.
Changes in version 1.27.15
o Update documentation of geneModelFromTxdb
Changes in version 1.27.14
o Add rmarkdown into Suggests
o update importScSeqScore.
Changes in version 1.27.13
o Fix the size by number when read from file.
Changes in version 1.27.12
o add decontructor to hic.cpp.
Changes in version 1.27.10
o split the vignette to multiple files.
Changes in version 1.27.9
o plot back to back Interaction Data Track
Changes in version 1.27.8
o fix the typo in hic.cpp
Changes in version 1.27.7
o figure out the error in dyn.load trackViewer.so
Changes in version 1.27.6
o add support for .hic and .cool for importGInteraction
Changes in version 1.27.5
o add importGInteraction
Changes in version 1.27.4
o change the re-sample method for viewTracks
Changes in version 1.27.3
o Update documentation.
o add label_on_feature for lolliplot
Changes in version 1.27.2
o Fix the bug for pie plot of dandelion.plot when introduce label.parameters.
Changes in version 1.27.1
o Fix the bug that if all scores are greater than 10 and all scores are integer.
Changes in version 1.25.4
o remove http_status from documentation.
Changes in version 1.25.4
o add function to split the lollipop plot into multiLayers.
Changes in version 1.25.3
o Fix the issue in AddArrowMark that grid changed the unit id.
Changes in version 1.25.2
o Fix the issue if there is interrupt of the internet connection to generate vignette.
Changes in version 1.25.1
o Provide more clearly warning or error message if the input is not sorted or contain NA values.
Changes in version 1.23.5
o remove import plot from graphics.
Changes in version 1.23.5
o replace class function by is function.
Changes in version 1.23.4
o fix a issue of "EXPR must be a length 1 vector".
Changes in version 1.23.3
o fix a issue of vignette when visit ebi proteins api.
Changes in version 1.23.2
o plot multiple genes in one track.
Changes in version 1.23.1
o add interactionData track.
Changes in version 1.21.18
o update NEWS file from "CHANGES IN VERSION" to "Changes in version".
Changes in version 1.21.17
o remove google scholar in vignette.
Changes in version 1.21.16
o Try to avoid the error introduced by BiocStyle: Invalid Parameter - /figure-html.
Changes in version 1.21.15
o Add google scholar in vignette.
Changes in version 1.21.14
o Update the citation in readme file.
Changes in version 1.21.13
o Fix a typo in plotLollipops.
Changes in version 1.21.12
o setTrackXscaleParam accept position attribute.
Changes in version 1.21.11
o set rescale of lolliplot by precentage.
Changes in version 1.21.10
o fix the bug of score is NumericList.
Changes in version 1.21.9
o accept negative values for bigwig files.
Changes in version 1.21.8
o update legend method.
Changes in version 1.21.7
o fix the label label.parameters.gp.
Changes in version 1.21.6
o add sample code of Proteins API.
Changes in version 1.21.5
o fix the bug that lollipop stem is too long.
Changes in version 1.21.4
o add shape for lolliplot.
Changes in version 1.21.3
o add shinyApp video.
Changes in version 1.21.2
o add citation.
Changes in version 1.21.1
o fix the bug if condiction with multiple logical values.
Changes in version 1.19.28
o fit the small size canvas.
Changes in version 1.19.27
o add safe color theme.
Changes in version 1.19.26
o update author info.
Changes in version 1.19.25
o change save and load name for browseTracks.
Changes in version 1.19.24
o add save and load for browseTracks.
o add swith dandelion height method (mean or count) for browseTracks.
Changes in version 1.19.23
o add color picker for pie.stack for browseTracks.
Changes in version 1.19.22
o fix the bug in legend for browseTracks.
Changes in version 1.19.21
o fix the bug of that can not set color for undefined for browseTracks.
Changes in version 1.19.20
o fix the bug of lable is not saved for browseTracks.
Changes in version 1.19.19
o fix the bug of output svg for browseTracks.
Changes in version 1.19.18
o add rotate 45 in color picker for browseTracks.
Changes in version 1.19.17
o add apply to all in color picker for browseTracks.
Changes in version 1.19.16
o fix the grammar in vignettes.
Changes in version 1.19.15
o update vignettes.
Changes in version 1.19.14
o update undo for browseTracks.
Changes in version 1.19.13
o add undo for browseTracks.
Changes in version 1.19.12
o add remove all guideline function.
Changes in version 1.19.11
o fix the fonts bug for export png in browseTracks
Changes in version 1.19.10
o remove all svgs before browseTracks
Changes in version 1.19.9
o Build shiny output objects for browseTracks
Changes in version 1.19.8
o add dandelion plots to browseTracks
Changes in version 1.19.7
o fix a bug in track class
o improve one-step visualization for browseTracks
Changes in version 1.19.6
o improve one-step visualization for browseTracks
o try to avoid the error caused by VariantAnnotation
Changes in version 1.19.5
o improve one-step visualization for browseTracks
Changes in version 1.19.4
o add one-step visualization for browseTracks
Changes in version 1.19.3
o adjust y label position for viewTracks
Changes in version 1.19.2
o adjust legent position for dandelion.plot
Changes in version 1.19.1
o add featureLayerID to dandelion.plot
Changes in version 1.17.8
o fix the bug in figure captions of vignette.
Changes in version 1.17.7
o allow ylim of tracks be not fixed from 0.
Changes in version 1.17.6
o fix a issue of circle in lollipop plot.
Changes in version 1.17.4
o add flag type in lollipop plot.
Changes in version 1.17.3
o adjust plot position for dandelion.plot.
Changes in version 1.17.2
o add Yscales for dandelion.plot.
Changes in version 1.17.1
o add smooth function for tracks.
Changes in version 1.15.13
o add feature.gr parameter to plotGInteractions.
Changes in version 1.15.12
o add new function plotGInteractions.
Changes in version 1.15.11
o update the title
Changes in version 1.15.10
o Change all "class" function to "is" function.
Changes in version 1.15.9
o Add lollipopData to tracks-class.
Changes in version 1.15.8
o Plot lollipop plot with tracks.
Changes in version 1.15.7
o Add new parameter rescale to lolliplot.
Changes in version 1.15.6
o Add new function geneTrack.
Changes in version 1.15.5
o fix the warning in windows documentation.
Changes in version 1.15.4
o fix the warning in windows documentation.
Changes in version 1.15.3
o fix the position of ylabs in plotOneIdeo.
Changes in version 1.15.2
o fix the bug in addGuideLine and viewTracks when plot tracks with breaks.
Changes in version 1.15.1
o fix the bug in dandelion.plot
o use Roxygen2 to generate help documents
o add new functions: getLocation, viewGene
Changes in version 1.13.11
o fix the bug maxgap could not be less than 0 in findOverlaps
Changes in version 1.13.10
o fix the bug documentation of ideogramPlot is different from the codes.
Changes in version 1.13.9
o fix the bug when using findOverlaps, when 'type' is "any",
at least one of 'maxgap' and 'minoverlap' must be set to its
default value
Changes in version 1.13.8
o automatic set the font size in ideogramPlot
Changes in version 1.13.7
o fix the bug in ideogramPlot when data range is identical for heatmap
layout.
Changes in version 1.13.6
o add draggable tracks in browseTracks function
Changes in version 1.13.5
o add arrow tools in browseTracks function
Changes in version 1.13.4
o add label tools in browseTracks function
Changes in version 1.13.3
o fix bugs in browseTracks function
Changes in version 1.13.2
o add more columns to GRoperator function
o add browseTracks function
Changes in version 1.11.8
o support break x-axis for viewTracks.
Changes in version 1.11.7
o improve the ideogramPlot function.
Changes in version 1.11.6
o improve the ideogramPlot function.
Changes in version 1.11.5
o add ideogramPlot function.
Changes in version 1.11.4
o remove the blank bottom space for lolliplot.
Changes in version 1.11.3
o fix a bug when tracks has multiple max values.
Changes in version 1.11.2
o add jitter label only for lolliplot.
Changes in version 1.11.1
o adjust the x postion of lolliplot.
Changes in version 1.9.14
o add controls for lolliplot yaxis.
Changes in version 1.9.13
o the height of features could be unit object.
Changes in version 1.9.12
o Update the vignette.
o Fix the position of ylab.
Changes in version 1.9.11
o Add caterpillar layout to lolliplot.
Changes in version 1.9.10
o Fix the bug that if the features is outside of granges for lolliplot.
Changes in version 1.9.9
o Fix the bug that no xscale is drawn when there is no positive value for track 1.
Changes in version 1.9.8
o lolliplot could accept multiple features for one layer.
Changes in version 1.9.7
o lolliplot could accept multiple types for multiple layers.
Changes in version 1.9.6
o fix the bugs for the lolliplot when the last snp need to be jittered.
Changes in version 1.9.5
o fix the bugs in the documentation.
Changes in version 1.9.4
o add pie.stack layout for lolliplot.
Changes in version 1.9.3
o add controls for lolliplot labels.
Changes in version 1.9.2
o update documentation to include the how to set ylim.
Changes in version 1.7.9
o fix the bug that legend write to outside.
Changes in version 1.7.8
o fix the typo in documentation.
o update the lollipop plot.
Changes in version 1.7.7
o add dandelion plot function.
Changes in version 1.7.6
o add legend for lollipop plot.
Changes in version 1.7.5
o add lables in the nodes of lollipop plot.
Changes in version 1.7.4
o Update documentation.
Changes in version 1.7.3
o add Y axis to lollipop plot.
Changes in version 1.7.2
o add lollipop plot!
Changes in version 1.7.1
o adjust the fontsize for optimizing styles with theme.
o add gene symbols if possible for geneModelFromTxdb.
Changes in version 1.5.6
o update documentation.
o add new feature for optimizing the styles with theme.
Changes in version 1.5.5
+ NEW FEATURES
o remove interactiveViewer from the package.
+ BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
Changes in version 1.5.4
+ NEW FEATURES
o parse2GRanges function to parse text into GRanges
+ BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
Changes in version 1.5.3
+ NEW FEATURES
o export importData function to import data to RleList.
+ BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
Changes in version 1.5.2
+ NEW FEATURES
o Add GRanges operators: +, -, *, /
o export parseWIG function.
+ BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
Changes in version 1.3.4
+ NEW FEATURES
o No changes classified as 'new features' (package under active
development)
+ BUG FIXES
o improve efficiency of importScore
Changes in version 1.3.3
+ NEW FEATURES
o could flip the x-axis if needed
+ BUG FIXES
o improve efficiency of interactiveViewer
Changes in version 1.3.2
+ NEW FEATURES
o No changes classified as 'new features' (package under active
development)
+ BUG FIXES
o fix bugs in importScore when format=="BigWig"
Changes in version 1.3.1
+ NEW FEATURES
o add new function plotGRanges for quick view GRanges data
o add ranges when importScore
+ BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)
Changes in version 1.1.1
+ NEW FEATURES
o addArrowMark with label
+ BUG FIXES
o No changes classified as 'bug fixes' (package under active
development)