CHANGELOG.md

0.17.0 (2024-05-06)

Features

• api: use gosling server instead of HiGlass server for gene search (#1053) (f0ec117)

Performance Improvements

• track: reduce webgl memory usage (#1057) (80ed16e)

0.16.0 (2024-02-22)

Bug Fixes

• core: Flipped y-axis stacked bar chart (#1042) (6f13ae7)

Performance Improvements

• track: Persist GoslingTrackModels (#1044) (560d121)

0.15.0 (2024-01-19)

Bug Fixes

• core: do not print unknown data type warnings in console (#1034) (dc0386d)
• core: publish events on first render (#1024) (bf470c1)
• track: prevent circular layout legend from being obscured (#1029) (e1649af)

Features

• core: export GoslingCompProps (#1033) (e4091ae)

0.14.0 (2024-01-08)

Performance Improvements

• core: stretch certain marks instead of redraw (#1018) (0b405ba), closes #1023

0.13.2 (2023-12-19)

Features

• core: export util functions for conversion to flat tracks (#1016) (85f0be1), closes #1017

0.13.1 (2023-12-12)

Bug Fixes

• core: editor deployment (#1010) (afb8ae4)
• core: pnpm deploy (#1009) (8e51fbe)
• track: Allows for tracks in stacked circular tracks to receive click events (#1005) (aea3a5d)

0.13.0 (2023-12-04)

Features

• core,track: move gosling-theme to this repo, support more compact genomic axis style (#996) (09c0179)
• core: export several util functions (#997) (7e9a834), closes #1001
• core: return a processed spec when a new spec is compiled (#1002) (59aed49)
• track: performance improvements (#988) (edd24de), closes #823

0.12.0 (2023-10-31)

Bug Fixes

• core: rename exports from .es.js to .js (#987) (f97269a)

Features

• api: publish traversed spec to gosling api (#978) (f17e69f)
• core: replace uuid dependency with crypto.randomUUID() (#976) (9b1e89b)

0.11.0 (2023-09-27)

0.10.4 (2023-09-27)

Bug Fixes

• core: preserve the zoom status only when needed (#974) (b74f10e)

Features

• data-fetcher,core: Add support for getting data from URLs that require certain request initializations (#965) (6ddb4b6)

0.10.3 (2023-09-25)

Bug Fixes

• core: first track ID should not be lost after compile (#972) (f73410d)

0.10.2 (2023-09-22)

Bug Fixes

• core: preserve zoom status when new track added (#971) (875a9b5)
• core: rule mark calculation in circular layout (#967) (09a5207)

0.10.1 (2023-08-02)

Bug Fixes

• data-fetcher: gmod/gff stream issue (#957) (c698785)

0.10.0 (2023-08-01)

Bug Fixes

• core: do not override ID in tracks from views (#954) (6654e0d)
• data-fetcher: correctly calculate the distance to previous mutation in VCF (DISTPREV) (#949) (ef5f58f)
• track: remove private properties from draw() (#952) (529e9a3)

Features

• api: consistent track/view IDs for JS API (#944) (1c2b766)
• api: onNewTrack, onNewView (#943) (a98ee69)
• api: subscription for genomic axis changes (#935) (a2c36f5)
• core, api, editor: support using view IDs (#939) (cd8d300)
• data-fetcher: GFF3 with tabix (#923) (526882f)
• track: dummy-track (#946) (ee02d38)

0.9.33 (2023-07-11)

Bug Fixes

• data-fetcher: Bump tabix-js version to fix errors when loading BED files (#938) (d901232)
• data-fetcher: support genomicFieldsToConvert (#932) (c94ecae)

0.9.32 (2023-07-05)

Bug Fixes

• fix duplicated data and odd tile load timing in the bam data fetcher (#927) (4e52907)

0.9.31 (2023-05-31)

Bug Fixes

• revert breaking React 18 changes (#913) (52bf2f2)

Features

• islandviewer improvements (#906) (86f50de)
• upgrade higlass to v1.12.4 (#902) (758f730), closes #903

0.9.30 (2023-05-11)

Bug Fixes

• fix inRange filter (#896) (13a70a2)
• pileup calculation works when start and end fields are the same (#891) (7754a15)
• tile values are correctly filtered based on genomics windows (#892) (cef7953)

Features

• add BED file datafetcher (#877) (a087340)
• add islandviewer example (#887) (897b0ef)
• support React 18 (#898) (dc13381)

0.9.29 (2023-04-26)

Bug Fixes

• alias lodash to lodash-es for smaller bundle (#879) (9f1d108)
• editor: reduce asset size (#859) (404bafa)
• flip the y-axis labels when the track is vertical (#862) (6bd6df2)

Features

• add jsx-a11y eslint plugin (#842) (5f12b66)
• editor: add link to gosling-lang.org to editor header (#855) (6964671)
• support optional INFO fields of VCF files (#864) (ebb5bea)
• upgrade to HiGlass 1.12.2 (#866) (0bc5691)

0.9.28 (2023-01-05)

Features

• infer chr prefix in bam file for ease of use (#837) (e3461cf)

0.9.27 (2022-12-08)

Bug Fixes

• correctly display legends when multiple tracks are overlaid (#834) (4ea1033)

Features

• add support for drawing vertical lines on withinLink (#833) (c4b4e9d)

0.9.26 (2022-11-26)

Bug Fixes

• do not try to infer tile unit size when info missing (#821) (7edb6c0)
• fix errors when displaying vcf files (#826) (95791a6)
• improve within link performance by reducing the number of event points (#828) (4562bc9)

0.9.25 (2022-10-14)

Bug Fixes

• fix an error when tilePos is undefined (#819) (635b531)
• fix build by adding pubsub (#820) (f4445c6)

0.9.24 (2022-09-16)

Features

• add type heirarchy for BarTrack (#808) (e00d145)
• show null DISTPREVLOGE from VCF files (#814) (e5282fc)

0.9.23 (2022-08-26)

Bug Fixes

• allow custom chromnames in zoomTo api (#794) (bf8948e)
• ensure to use non-null hgRef (#804) (9978eb8), closes #805
• fix displace transform on non-higlass data (#802) (3c3b52b)
• support using custom chromosome names in genomic domains (GenomicDomain); fix zoomTo() (#796) (5ea2355)

Features

• add TabularDataFetcher interface (#803) (330278f)

0.9.22 (2022-08-06)

Bug Fixes

• correctly infer relative genomic positions in tooltip using assembly (#770) (a81be97)
• editor: use correct field names in circos example (#772) (29bb840)
• use consistent letter case for data types (e.g., JSONData → JsonData) (#773) (4fa101d)

Features

• api: capture mouseover event on a track; click event on a linear track (#774) (21edf06)
• api: get track information; correctly use assembly in zoom APIs (#777) (e4c3d1f)
• enable using custom assembly by specifying chrom sizes (#776) (b08334a)
• make column, position, row properties optional for bigwig, vector, and multivec (#769) (978a2b3)
• make width and height of track optional (#779) (a52d969)
• run pre-commit hooks in parallel (#784) (edefd8e)

0.9.21 (2022-07-14)

Bug Fixes

• change worker directory from .js to .ts to inject the buffer shim (#763) (351bbe4)
• data-fetchers: fix error using Buffer in VCF worker (#758) (007c3e1)
• do not make marks disappear when zoomed in very far (#765) (9d279ed)

0.9.20 (2022-07-03)

Bug Fixes

• editor: fix typo on the mouse event example (#726) (c7be92d)
• fix error when using latest gosling.js by pinning generic-filehandle (#737) (dec0e64)
• include types to the bundle; exclude editor types (#749) (1935062)
• override RemoteFile.read to be more flexible (#743) (d27fed4)

Features

• add partial types for HGC (#728) (3364b15)
• data-fetchers: migrate BAM worker to TS (#739) (20e989c)
• data-fetchers: migrate bigwig to TS (#741) (e52b594)
• data-fetchers: migrate VCF data-fetcher to TS (#740) (4aba4df)

0.9.19 (2022-06-09)

Bug Fixes

• editor: minor bugs when importing & exporting examples (#701) (1fcea27)
• fix json track errors due to using undefined mRangeBrush (#716) (2ebde84)
• gist example with jscode (#684) (a94e1c1)
• out of memory when deploy (#680) (9253f48)
• remove legend layer in remove(); do not render twice on Editor when example ID is specified in URL (#686) (d3f22c9)
• use assembly in vcf data fetcher (#698) (a2440f6)

Features

• capture mouse events on marks for tooltips, hovering effects, and APIs (#667) (0b67659)
• editor: compact side panel buttons (#721) (c2526ca)
• editor: preserve spec in session storage (#722) (8597739)
• editor: support javascript editor (#671) (410d049)
• editor: use current hostname and path for SAVE URL (#690) (7507172)
• editor: visualize JS spec using Gist URL (#704) (0b4c86a)
• enable adding a root level aria-label using description (#723) (88f8894)
• genomic range selection in linear tracks (#693) (8d89b60)
• support indels in VCF (#699) (377e509)
• support VCF with Tabix (#689) (84d9213)
• treeshake pkg info in module export (#694) (a12d454)
• turn off mouse events by default; rename API keys; rename and restructure mouse event properties (#712) (feec1d9)

0.9.18 (2022-05-06)

Bug Fixes

• fix crash on matrix example (#674) (0de295c)
• revert back to use gMain in gosling-brush (753a555)

Features

• add data transform to infer sv types (#676) (f31e888)
• add straight link for circular withinLink (#647) (02a60ef)
• allow checking the container size or aspect ratio for using responsive spec (#652) (7555ab7)
• allow using one side of diagonal of matrix (#644) (9c19f72)
• editor: add a showcase modal view (#657) (8a56c5e)
• editor: add export to html file (#672) (ddbd1e2)
• editor: gallery sidebar (#659) (da5a0c6)
• replace jest with vitest (#666) (e8eef28)
• support brushes on color legends (#663) (f76a3e5)
• support clipping rows when using bars (#643) (f858853)
• treeshake pkg info in module export (#665) (9ca746f)
• use reactive rendering for responsive specs (#645) (c00f4f8)

0.9.17 (2022-02-21)

Features

• editor: add options to change screen dimensions (#632) (5f2b67a)
• experimental: allow defining alternative specs for responsive visualization (#624) (458cc90)
• support 2D annotations using json data (#641) (efb1690)
• support checking aspectRatio to use responsive spec (#635) (ea96bc0)

0.9.16 (2022-01-31)

Features

• add hot and pink color schemes (#629) (9b170a7)
• support yDomain for 2D tracks (#627) (8675fdc)

0.9.15 (2022-01-24)

Features

• add responsive sizing options (#617) (0470dd0)
• support horizontal rules on matrix (#620) (b205fef)
• support native matrix visualization (#612) (d9c967c)
• support responsive resizing in circular layouts (#623) (cabaa51)
• use HiGlass heatmap for conventional 2D matrix (#615) (93fac44)

0.9.14 (2021-12-12)

Bug Fixes

• correct bezier curve condition for if statement (f525927)
• fix circular brush hiccup upon dragging (#607) (50d7ee4)

0.9.13 (2021-12-10)

Bug Fixes

• correctly show arcs when x is larger than xe (#605) (3d8fa38)
• do not filter out small withinLink marks by default (#604) (dabecd7)
• do not generate gosling model with undefined tilePos (#603) (42439a8)

Features

• allow aggregation functions (mean and sum) for vector, bigwig, and multivec (#591) (5ace48d)
• horizontal and vertical rule marks in linear layout (#601) (4eca209), closes #602 #603 #604 #591

0.9.12 (2021-12-09)

Features

• allow tooltip and mouse events on circular arc (#602) (40d8809)

0.9.11 (2021-11-29)

Bug Fixes

• ensure to assign proper uids to overlaid tracks (#598) (066c0d2)

0.9.10 (2021-11-29)

Features

• add available theme names to theme.schema.json (#570) (5115859)
• allow extracting splice junctions from BAM, flat withinLink, toward supporting sashimi plot (#586) (a6ef69e)
• infer SV types and find mates from bam files; add an API to get raw data in JSON format (#556) (2e2fd79)
• show loading messages in BAM tracks (#593) (bc9846f), closes #594
• update higlass.schema.json upon changes on its TS file (#594) (23b7393)
• use a default theme in gosling-track when missing (#584) (5b1c242)

0.9.9 (2021-10-25)

Bug Fixes

• fix errors with process and global when gosling.js package is used externally (#554) (6b3a564)
• inject Buffer polyfill for BamWorker (#537) (e8c792c)
• refer to actual track size instead of spec.width and spec.height for track encoding (#517) (70ace60)
• visibility affects on rect and rules; add padding to API types (#512) (2c134ed)

Features

• unknown assembly does not display chrN: on the genomic axis (#532) (19ad4d4)
• add gosling.js/embed package export (#524) (0439755)
• allow access to HiGlass ref from JS API (#558) (2f372ee)
• api: support searching for a gene position (#567) (05b82bd)
• built-in min and max columns for multivec and vector (#519) (41e48d4)
• editor: add a small triangle at the right-end of dropdown menu for affordance (#520) (7ed9a35)
• editor: support using relative CSV file URLs for Gist specs (#540) (af5f08e)
• enable auto doc generate (#503) (de231fe)
• migrate uuid & box-intersect to browser-compatible deps (#527) (d1fbbb3), closes #532
• more precise channel types (e.g., X, Y, and Color instead of Channel) (#533) (aa2cd62)
• remove aliases & update gmod deps (#526) (6be5195)
• support ye with bar (#518) (ef0fd59), closes #517 #519
• support specifying zoom limits (zoomLimits) (#521) (0517bc5), closes #522 #505 #511 #526
• support viewing paired reads in BAM files (#538) (109d119), closes #536 #537
• unify ESM/UMD build and development with Vite (#522) (ac7722c), closes #505 #511

0.9.8 (2021-08-30)

Bug Fixes

• app crash on overriding themes (#490) (8d9cd9e)
• do not touch original spec when compiling (#489) (22a0f31), closes #488

Features

• add reactive rendering as an experimental option (#488) (aeb2269)
• include mouse position visibility to the theme (#491) (5d30675)

0.9.7 (2021-08-28)

Bug Fixes

• handle embed and use the previous component structure (#486) (143b916)

0.9.6 (2021-08-28)

Bug Fixes

• get chr sizes directly from bam files (#483) (f4a2482)

Features

• reactive rendering (#484) (abc2851)

0.9.5 (2021-08-27)

Bug Fixes

• errors when using "json" data (#481) (473fbd0)

0.9.4 (2021-08-26)

Bug Fixes

• accurately fetch data when data and/or dataTransform is defined in individual tracks that are overlaid (#470) (e647386)
• brushes work correctly regardless of the position of its parent track (#474) (3c4af0f)
• editor: do not show default demo before loading gist spec (#472) (04335ae)

Features

• allow click events; add padding for zoomTo APIs (#477) (ffca961)
• bai file url is required (#480) (0e601be)
• capture mouse hover event on arcs (#476) (47fffbe)
• change cursor style upon mouse hover on marks (#478) (ac9c0b5)

0.9.3 (2021-08-18)

Features

• inline bam worker to the bundle (#467) (95d4f1f)

0.9.2 (2021-08-17)

Features

• add explicit PartialTrack def to schema (#466) (c5c9be5)

0.9.1 (2021-08-14)

Features

• enable showing track titles in circular layouts (#464) (e223377)
• responsive quantitative color legend for compact tracks (#462) (9d56cbe)

0.9.0 (2021-08-10)

Features

• api: getCanvas() (#452) (68637db)
• support vertical tracks (#451) (3b502c5)

0.8.13 (2021-08-05)

Features

• expressive BAM rendering (#446) (90c758b)
• support templates, enable precise and correct track/view sizing and triangle positioning (#445) (aef4657), closes #446

0.8.12 (2021-07-26)

0.8.10 (2021-07-26)

Bug Fixes

• draw circular background on the back, not in front of some tiles (#441) (b12f19d)
• ensure the entire height a multiple of 8 (#442) (91f0dae)

0.8.9 (2021-07-20)

Bug Fixes

• safely use default values when theme in undefined (#437) (67d124b)

0.8.8 (2021-07-19)

Features

• add more theme components like dashed grid, font styles, background colors (#436) (1881e7d)

0.8.7 (2021-07-12)

Features

• support more parameters in embed() function (#435) (805fd3d)

0.8.6 (2021-07-12)

Features

• separating theme from the main grammar (#434) (bda3a77)

0.8.5 (2021-07-09)

Bug Fixes

• convert to numbers when quantitative fields are strings (#402) (95212bd)
• editor: address hiccups in editor (#411) (3025533)
• remove improper loading message in track (#418) (62bf073)

Features

• add margin and border as props of GoslingComponent (#420) (4df2b2e)
• add a between-link mark (#405) (c7a76e2)
• allow specifying id and className in GoslingComponent (#419) (30d45a3)
• api: zoom to extent (#408) (0b3c71f)
• background of circular tracks, legend titles, and better brush style (#429) (e469efe)
• rename link marks to betweenLink and withinLink (#416) (8e7556c)

0.8.3 (2021-05-28)

Features

• allow vertical band connection w/o independent scales yet (#394) (5591e2d)
• api: support mouseover event listener (#388) (e56e32c)

0.8.2 (2021-05-25)

Bug Fixes

• reduce log warning messages (#392) (4a14d7a)

Features

• support tooltips for most marks in linear, relative genomic position, formatting (#387) (824faba)

0.8.1 (2021-05-19)

Bug Fixes

• properly refresh grids upon zoom (#381) (7cc61c3)

Features

• api: export pdf file (#385) (42c1d99)
• api: export png file (#382) (5799c96)
• editor: change editor theme depending on the theme of gosling spec (#380) (fa9f921)
• Support bam files (#374) (7adbddf)

0.8.0 (2021-05-04)

Features

• data transformation for string concat and replace (#366) (9cb313e)
• expose mouse position color to theme and change default color (#376) (85fea1d)
• select example through url (#367) (0c87602)
• show grid for quantitative y axis (#377) (fd6e181)
• show quantitative color legends (#375) (d3782de)
• support defining custom themes (#370) (9a628f9)
• support overriding and customizing theme (#365) (c6897e1)
• support y-axis (#373) (d049f9e)

0.7.7 (2021-04-19)

Features

• add 'about' model view (#347) (53cb362)
• add exon split transformation (#364) (1413494)
• allow defining track styles in the upper level (#363) (d00b871)
• api: allow specifying transition duration in zoom (#358) (78db378)
• support a dark theme (#359) (2248fc4)

0.7.6 (2021-04-13)

Features

• api: zoom to genomic position (#356) (48f3311)

0.7.5 (2021-04-13)

Features

• api: zoom to gene (#353) (3021b82)
• data transform as ordered array (#355) (38ed0e4)
• enable customizing stroke of brush (#352) (b713b94)

0.7.4 (2021-04-12)

Features

• consider filtering specs during fetching tilesets (#339) (3b67a85)
• define type of chromosome in domain (#348) (6ab6cf7)
• support log transformation (#344) (b6155ce)
• support piling up transcript annotations (#346) (f61649b)

0.7.3 (2021-04-07)

Features

• support tooltips in linear rect and point (#337) (c8d64c1)

0.7.2 (2021-04-07)

Bug Fixes

• text-align left to gosling component (#332) (0e2247d)

Features

• add mark displacement options (#320) (8ead36b)
• examples with overriding view props in tracks (#327) (3458712)
• support higlass matrix visualization (#321) (1094142)
• vertical track (#325) (f0b95f9)

0.7.1 (2021-03-06)

Bug Fixes

• allow using track title in circular layouts (#315) (0dd06a8)

Features

• editor: allow clicking on the title to open a new tab (#312) (275d757)

0.7.0 (2021-03-03)

Bug Fixes

• initially compile no-desc gist (9a2d05d)

0.1.1 (2021-03-03)

Bug Fixes

• arrangement is overriden from parents (#248) (7c589d1)
• close description and code panels in narrow screen (#288) (ee88abb)
• correctly auto-generate gosling.schema.json (#234) (d89c0d8)
• show dropdown menu and disable screen zoom for proper pinch zoom in visualizations in mobile (#289) (28f2047)

Features

• add error boundary to avoid crash (#247) (8a17d1b)
• add gist link icons and support github flavored md (#301) (cd74497)
• flip y axis if the last track in a view is using link marks (#256) (a4fe34c)
• loading specs from gist (#263) (8a702f3)
• support an inline legend and 'unknown' type assembly (#252) (2ed5ea7)
• switch to use glasbey for many categories (#302) (fb4382e)

0.1.0 (2021-02-20)

0.0.26 (2021-02-19)

Bug Fixes

• correctly calculate position of tracks considering overlayOnPreviousTrack (#227) (e2e5b9a)

0.0.25 (2021-02-17)

Bug Fixes

• address a problem when importing a gosling.js package (c07e3bd)
• do not crash editor when random color str is used (#211) (c39873e)
• encode width of triangle same as its height by defualt (#220) (5602e99)
• remove track-level layout definition to prevent using different layouts for tracks in a same view (#214) (be1eaf8)

Features

• allow resizing font in editor (#216) (f237e11)
• support BigWig (#196) (48d5ff4)
• use relative arrangement (#198) (4888b81)

0.0.24 (2021-02-08)

0.0.23 (2021-02-08)

0.0.22 (2021-02-08)

Features

• reduce the pkg size by specifying external libs (#192) (03f4a04)

0.0.21 (2021-02-08)

0.0.20 (2021-02-08)

Features

• modify dependency to make the pkg light-weighted (#191) (e7c3b88)

0.0.19 (2021-02-08)

Features

• support embedding a Gosling component to a HTML element (#190) (d5f63c1)

0.0.18 (2021-02-07)

Bug Fixes

• use corret json values type (76cac9f)

0.0.17 (2021-02-07)

Bug Fixes

• correctly draw links when strokeWidth is zero (#186) (b968579)
• default static option for circular layouts is true (#153) (f490765)
• position text on the exact middle (#172) (f2dd2a2)
• properly sort data before area (#173) (8e92557)

Features

• add a data preview panel in the editor (#175) (137b5eb)
• support genome builds (#178) (79a8fd0)
• support multiple visibility options (#159) (fe60459)
• support using superpose with multiple datasets (38967eb)

0.0.16 (2021-01-24)

Bug Fixes

• layout of axis and its track should be the same (#119) (83ae75e)

Features

• make plugin axis and brush tracks visible in the package (34bcaa7)

0.0.15 (2021-01-22)

Bug Fixes

• prevent from crash due to unsafe IsDataTrack checking (5068903)
• use absolute height of rect in circular layout when size is provided (#109) (93ef22b)

Features

• allow showing axis in circular tracks (#110) (b14769e)
• circular brush (#106) (8c6001f)

0.0.14 (2021-01-11)

Bug Fixes

• correctly calculate arrangement of tracks (04d68a9)
• correctly calculate layout when title is specified (#82) (b2e0130)
• do not show y-axis since it is not prepared yet (#94) (c130edd)
• remove rows where chr info is incorrectly parsed (#67) (1a703ec)
• superposeOnPreviousTrack of first track is always false (#71) (3f5aa99)
• unique editor urls for custom specs work correctly (#60) (f017ef6)
• update control points for clearer bezier curves (#72) (a9ec5f7)

Features

• adaptive axis format considering width/height of track (#58) (43df1e9)
• support basic templates for given data type (#96) (81d59eb)
• support turning on/off auto run in editor (#62) (b79c20d)

0.0.13 (2020-12-26)

0.0.12 (2020-12-26)

0.0.11 (2020-12-26)

0.0.10 (2020-12-26)

Bug Fixes

• add actions/checkout before deploy (52270eb)
• better default for innerRadius and outerRadius (#45) (ff58f0f)
• build before deploy (8afe635)
• correct url for deploy workflow (53011bc)
• use access token (a377398)

Features

• allow encoding data to strokeWidth and opacity (#44) (fb8a7f8)
• allow svg export for rect (#42) (14a587a)
• improve editor ui (#55) (f8d3b58)
• title and subtitle of view (#47) (d7256e7)
• unique url to display a custom spec in the editor (#51) (f701126)

0.0.8 (2020-12-18)

0.0.7 (2020-12-18)

0.0.3 (2020-12-09)

0.0.1-beta5 (2020-12-09)

0.0.1-beta4 (2020-11-30)

0.0.1-beta3 (2020-11-25)

0.0.1-beta2 (2020-11-24)

0.0.1-beta1 (2020-11-23)