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)