NEWS

---

trackViewer 1.43.5

• Add line and histogram to tracktype for trackstlye.

trackViewer 1.43.4

• Remove the clip for annotation track.

trackViewer 1.43.3

• Add documentation to remove y label.

trackViewer 1.43.2

• Make it possible to plot annotation for peak regions.

trackViewer 1.43.1

• Make it possible to plot link for back2back interaction data.

trackViewer 1.41.10

• Improve the plot speed for interaction data.

trackViewer 1.41.9

• Add a simple gene track plot model.

trackViewer 1.41.8

• Add listNormalizations function.

trackViewer 1.41.7

• Fix the bug that newpage parameter not used for plotGRanges.

trackViewer 1.41.6

• Add 'legendPosition' parameter for lollipop plot.

trackViewer 1.41.5

• Export the method '$' for trackStyle class.

trackViewer 1.41.4

• Move the 3d plots to a different package.

trackViewer 1.41.3

• plot lolliplot with multiple shapes in one position.

trackViewer 1.41.2

• export view3dStructure function.

trackViewer 1.41.1

• Add mdsPlot function.

trackViewer 1.39.17

• Fix the legend with alpha for lolliplot.

trackViewer 1.39.16

• Import txdbmaker.

trackViewer 1.39.15

• Optimize the reduce function for loopBouquetPlot.

trackViewer 1.39.14

• reduce the input for loopBouquetPlot.

trackViewer 1.39.13

• Handle the empty input for loopBouquetPlot.

trackViewer 1.39.12

• Update the safe text algorithm for loopBouquetPlot.

trackViewer 1.39.11

• Add parameter safe_text_force for loopBouquetPlot.

trackViewer 1.39.10

• Add color for geneTrack.

trackViewer 1.39.9

• Fix multiple bugs in loopBouquetPlot.

trackViewer 1.39.8

• Change loopBouquetPlot to grid plot.

trackViewer 1.39.7

• Fix the example for loopBouquetPlot.

trackViewer 1.39.6

• add loopBouquetPlot.

trackViewer 1.39.5

• Browse heatmap by js (scratch).

trackViewer 1.39.4

• Fix the issue if the first label is empty for lolliplot.

trackViewer 1.39.3

• Fix the mismatch data track when change the ylim in browseTracks.

trackViewer 1.39.2

• Fix the wrong plot for multiple genes track in browseTracks.

trackViewer 1.39.1

• Fix the y-axis for lollipop plot.

trackViewer 1.37.15

• Fix reading valid pairs typo.

trackViewer 1.37.14

• update the lollipopPlot documentation to fix the issue unable to find an inherited method for function 'content' for signature 'response'.

trackViewer 1.37.13

• fix the feature legend space.

trackViewer 1.37.12

• add ARA function.
• fix the missleading color legend of interaction data.
• fix the bug in addInteractionAnnotation.

trackViewer 1.37.11

• fix the minimal font of optimized style.

trackViewer 1.37.10

• add function GIoperator.

trackViewer 1.37.9

• add function addInteractionAnnotation for Interaction data.

trackViewer 1.37.8

• change the filter condiction for tads annotation of Interaction data.

trackViewer 1.37.7

• add tads annotation for Interaction data.

trackViewer 1.37.6

• add lollipop_style_switch_limit for lollipop plot.

trackViewer 1.37.5

• add border_color for Interaction data.

trackViewer 1.37.4

• update the documentation for lollipopPlot for changes of the snp label.

trackViewer 1.37.3

• use strawr to replace the local C++ script.

trackViewer 1.37.2

• remove the CXX_STD = CXX11 from straw Makevars.

trackViewer 1.37.1

• add stop message when there is negative values for grid.pie plot.

trackViewer 1.35.5

• use straw for hic import.

trackViewer 1.35.4

• handel label.parameter.draw for labels.

trackViewer 1.35.3

• Add documentation for selected labels for mutations.

trackViewer 1.35.2

• Add support for node label parameters.

trackViewer 1.35.1

• Add support for single resolution cooler file.

trackViewer 1.33.8

• Fix a bug if there is no name for the freatures.

trackViewer 1.33.7

• print the more pseudocode in browseTracks.

trackViewer 1.33.6

• Fix the bug for 'invalid color name' in browseTracks
• print the pseudocode in browseTracks

trackViewer 1.33.5

• Change the cool file open flag to "H5F_ACC_RDONLY"

trackViewer 1.33.4

• Fix a issue for plot tracks by insert 0 to the first signals.

trackViewer 1.33.3

• Add support for motif logo for lollipop plot.

trackViewer 1.33.2

• Add support for multiple operators for viewTrack.

trackViewer 1.33.1

• Fix the bug when locateScale return NA values.

trackViewer 1.31.4

• Fix the issue in windows 2022.

trackViewer 1.31.2

• Handle the issue with long tail.

trackViewer 1.31.1

• Move the heatmap legend to yaxis.

trackViewer 1.29.8

• Fix the a typo in read hic data.

trackViewer 1.29.7

• Fix the bug 'breaks' are not unique

trackViewer 1.29.6

• Add smooth curve to the tracks.

trackViewer 1.29.5

• Improve gene track plots.

trackViewer 1.29.4

• Fix the issue for auto-rescale lolliplot by emphasizing exon region when there are continues exons.

trackViewer 1.29.3

• Add the possibility to lolliplot to emphasize exon or intron region.

trackViewer 1.29.2

• Fix the yaxis when user supplied yaxis is greater than max scores.

trackViewer 1.29.1

• Update documentation lolliplot for rescale parameter.

trackViewer 1.27.15

• Update documentation of geneModelFromTxdb

trackViewer 1.27.14

• Add rmarkdown into Suggests
• update importScSeqScore.

trackViewer 1.27.13

• Fix the size by number when read from file.

trackViewer 1.27.12

• add decontructor to hic.cpp.

trackViewer 1.27.10

• split the vignette to multiple files.

trackViewer 1.27.9

• plot back to back Interaction Data Track

trackViewer 1.27.8

• fix the typo in hic.cpp

trackViewer 1.27.7

• figure out the error in dyn.load trackViewer.so

trackViewer 1.27.6

• add support for .hic and .cool for importGInteraction

trackViewer 1.27.5

• add importGInteraction

trackViewer 1.27.4

• change the re-sample method for viewTracks

trackViewer 1.27.3

• Update documentation.
• add label_on_feature for lolliplot

trackViewer 1.27.2

• Fix the bug for pie plot of dandelion.plot when introduce label.parameters.

trackViewer 1.27.1

• Fix the bug that if all scores are greater than 10 and all scores are integer.

trackViewer 1.25.4

• remove http_status from documentation.
• add function to split the lollipop plot into multiLayers.

trackViewer 1.25.3

• Fix the issue in AddArrowMark that grid changed the unit id.

trackViewer 1.25.2

• Fix the issue if there is interrupt of the internet connection to generate vignette.

trackViewer 1.25.1

• Provide more clearly warning or error message if the input is not sorted or contain NA values.

trackViewer 1.23.5

• remove import plot from graphics.
• replace class function by is function.

trackViewer 1.23.4

• fix a issue of "EXPR must be a length 1 vector".

trackViewer 1.23.3

• fix a issue of vignette when visit ebi proteins api.

trackViewer 1.23.2

• plot multiple genes in one track.

trackViewer 1.23.1

• add interactionData track.

trackViewer 1.21.18

• update NEWS file from "CHANGES IN VERSION" to "Changes in version".

trackViewer 1.21.17

• remove google scholar in vignette.

trackViewer 1.21.16

• Try to avoid the error introduced by BiocStyle: Invalid Parameter - /figure-html.

trackViewer 1.21.15

• Add google scholar in vignette.

trackViewer 1.21.14

• Update the citation in readme file.

trackViewer 1.21.13

• Fix a typo in plotLollipops.

trackViewer 1.21.12

• setTrackXscaleParam accept position attribute.

trackViewer 1.21.11

• set rescale of lolliplot by precentage.

trackViewer 1.21.10

• fix the bug of score is NumericList.

trackViewer 1.21.9

• accept negative values for bigwig files.

trackViewer 1.21.8

• update legend method.

trackViewer 1.21.7

• fix the label label.parameters.gp.

trackViewer 1.21.6

• add sample code of Proteins API.

trackViewer 1.21.5

• fix the bug that lollipop stem is too long.

trackViewer 1.21.4

• add shape for lolliplot.

trackViewer 1.21.3

• add shinyApp video.

trackViewer 1.21.2

• add citation.

trackViewer 1.21.1

• fix the bug if condiction with multiple logical values.

trackViewer 1.19.28

• fit the small size canvas.

trackViewer 1.19.27

• add safe color theme.

trackViewer 1.19.26

• update author info.

trackViewer 1.19.25

• change save and load name for browseTracks.

trackViewer 1.19.24

• add save and load for browseTracks.
• add swith dandelion height method (mean or count) for browseTracks.

trackViewer 1.19.23

• add color picker for pie.stack for browseTracks.

trackViewer 1.19.22

• fix the bug in legend for browseTracks.

trackViewer 1.19.21

• fix the bug of that can not set color for undefined for browseTracks.

trackViewer 1.19.20

• fix the bug of lable is not saved for browseTracks.

trackViewer 1.19.19

• fix the bug of output svg for browseTracks.

trackViewer 1.19.18

• add rotate 45 in color picker for browseTracks.

trackViewer 1.19.17

• add apply to all in color picker for browseTracks.

trackViewer 1.19.16

• fix the grammar in vignettes.

trackViewer 1.19.15

• update vignettes.

trackViewer 1.19.14

• update undo for browseTracks.

trackViewer 1.19.13

• add undo for browseTracks.

trackViewer 1.19.12

• add remove all guideline function.

trackViewer 1.19.11

• fix the fonts bug for export png in browseTracks

trackViewer 1.19.10

• remove all svgs before browseTracks

trackViewer 1.19.9

• Build shiny output objects for browseTracks

trackViewer 1.19.8

• add dandelion plots to browseTracks

trackViewer 1.19.7

• fix a bug in track class
• improve one-step visualization for browseTracks

trackViewer 1.19.6

• improve one-step visualization for browseTracks
• try to avoid the error caused by VariantAnnotation

trackViewer 1.19.5

• improve one-step visualization for browseTracks

trackViewer 1.19.4

• add one-step visualization for browseTracks

trackViewer 1.19.3

• adjust y label position for viewTracks

trackViewer 1.19.2

• adjust legent position for dandelion.plot

trackViewer 1.19.1

• add featureLayerID to dandelion.plot

trackViewer 1.17.8

• fix the bug in figure captions of vignette.

trackViewer 1.17.7

• allow ylim of tracks be not fixed from 0.

trackViewer 1.17.6

• fix a issue of circle in lollipop plot.

trackViewer 1.17.4

• add flag type in lollipop plot.

trackViewer 1.17.3

• adjust plot position for dandelion.plot.

trackViewer 1.17.2

• add Yscales for dandelion.plot.

trackViewer 1.17.1

• add smooth function for tracks.

trackViewer 1.15.13

• add feature.gr parameter to plotGInteractions.

trackViewer 1.15.12

• add new function plotGInteractions.

trackViewer 1.15.11

• update the title

trackViewer 1.15.10

• Change all "class" function to "is" function.

trackViewer 1.15.9

• Add lollipopData to tracks-class.

trackViewer 1.15.8

• Plot lollipop plot with tracks.

trackViewer 1.15.7

• Add new parameter rescale to lolliplot.

trackViewer 1.15.6

• Add new function geneTrack.

trackViewer 1.15.5

• fix the warning in windows documentation.

trackViewer 1.15.4

• fix the warning in windows documentation.

trackViewer 1.15.3

• fix the position of ylabs in plotOneIdeo.

trackViewer 1.15.2

• fix the bug in addGuideLine and viewTracks when plot tracks with breaks.

trackViewer 1.15.1

• fix the bug in dandelion.plot
• use Roxygen2 to generate help documents
• add new functions: getLocation, viewGene

trackViewer 1.13.11

• fix the bug maxgap could not be less than 0 in findOverlaps

trackViewer 1.13.10

• fix the bug documentation of ideogramPlot is different from the codes.

trackViewer 1.13.9

• fix the bug when using findOverlaps, when 'type' is "any", at least one of 'maxgap' and 'minoverlap' must be set to its default value

trackViewer 1.13.8

• automatic set the font size in ideogramPlot

trackViewer 1.13.7

• fix the bug in ideogramPlot when data range is identical for heatmap layout.

trackViewer 1.13.6

• add draggable tracks in browseTracks function

trackViewer 1.13.5

• add arrow tools in browseTracks function

trackViewer 1.13.4

• add label tools in browseTracks function

trackViewer 1.13.3

• fix bugs in browseTracks function

trackViewer 1.13.2

• add more columns to GRoperator function
• add browseTracks function

trackViewer 1.11.8

• support break x-axis for viewTracks.

trackViewer 1.11.7

• improve the ideogramPlot function.

trackViewer 1.11.6

• improve the ideogramPlot function.

trackViewer 1.11.5

• add ideogramPlot function.

trackViewer 1.11.4

• remove the blank bottom space for lolliplot.

trackViewer 1.11.3

• fix a bug when tracks has multiple max values.

trackViewer 1.11.2

• add jitter label only for lolliplot.

trackViewer 1.11.1

• adjust the x postion of lolliplot.

trackViewer 1.9.14

• add controls for lolliplot yaxis.

trackViewer 1.9.13

• the height of features could be unit object.

trackViewer 1.9.12

• Update the vignette.
• Fix the position of ylab.

trackViewer 1.9.11

• Add caterpillar layout to lolliplot.

trackViewer 1.9.10

• Fix the bug that if the features is outside of granges for lolliplot.

trackViewer 1.9.9

• Fix the bug that no xscale is drawn when there is no positive value for track 1.

trackViewer 1.9.8

• lolliplot could accept multiple features for one layer.

trackViewer 1.9.7

• lolliplot could accept multiple types for multiple layers.

trackViewer 1.9.6

• fix the bugs for the lolliplot when the last snp need to be jittered.

trackViewer 1.9.5

• fix the bugs in the documentation.

trackViewer 1.9.4

• add pie.stack layout for lolliplot.

trackViewer 1.9.3

• add controls for lolliplot labels.

trackViewer 1.9.2

• update documentation to include the how to set ylim.

trackViewer 1.7.9

• fix the bug that legend write to outside.

trackViewer 1.7.8

• fix the typo in documentation.
• update the lollipop plot.

trackViewer 1.7.7

• add dandelion plot function.

trackViewer 1.7.6

• add legend for lollipop plot.

trackViewer 1.7.5

• add lables in the nodes of lollipop plot.

trackViewer 1.7.4

• Update documentation.

trackViewer 1.7.3

• add Y axis to lollipop plot.

trackViewer 1.7.2

• add lollipop plot!

trackViewer 1.7.1

• adjust the fontsize for optimizing styles with theme.
• add gene symbols if possible for geneModelFromTxdb.

trackViewer 1.5.6

• update documentation.
• add new feature for optimizing the styles with theme.

trackViewer 1.5.5

• NEW FEATURES o remove interactiveViewer from the package.
• BUG FIXES o No changes classified as 'bug fixes' (package under active development)

trackViewer 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)

trackViewer 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)

trackViewer 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)

trackViewer 1.3.4

• NEW FEATURES o No changes classified as 'new features' (package under active development)
• BUG FIXES o improve efficiency of importScore

trackViewer 1.3.3

• NEW FEATURES o could flip the x-axis if needed
• BUG FIXES o improve efficiency of interactiveViewer

trackViewer 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"

trackViewer 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)

trackViewer 1.1.1

• NEW FEATURES o addArrowMark with label
• BUG FIXES o No changes classified as 'bug fixes' (package under active development)