From d427da2f05bb0b3522c23051415566af9b26461c Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Fri, 1 Nov 2024 10:34:41 -0700 Subject: [PATCH 01/31] Install dependency module for word cloud effect --- package.json | 1 + yarn.lock | 186 +++++++++++++++++++++++++++++++++++++++++++++++++-- 2 files changed, 183 insertions(+), 4 deletions(-) diff --git a/package.json b/package.json index f0e11d87..e5ac6643 100644 --- a/package.json +++ b/package.json @@ -32,6 +32,7 @@ "react-scripts": "5.0.1", "react-table": "^7.7.0", "react-tooltip": "^5.11.2", + "react-wordcloud": "^1.2.7", "redux": "^4.0.1", "redux-thunk": "^2.3.0", "tocbot": "^4.25.0", diff --git a/yarn.lock b/yarn.lock index 106f3f8c..09170453 100644 --- a/yarn.lock +++ b/yarn.lock @@ -1835,7 +1835,7 @@ schema-utils "^4.2.0" source-map "^0.7.3" -"@popperjs/core@^2.10.2", "@popperjs/core@^2.11.6": +"@popperjs/core@^2.10.2", "@popperjs/core@^2.11.6", "@popperjs/core@^2.9.0": version "2.11.8" resolved "https://registry.yarnpkg.com/@popperjs/core/-/core-2.11.8.tgz#6b79032e760a0899cd4204710beede972a3a185f" integrity sha512-P1st0aksCrn9sGZhp8GMYwBnQsbvAWsZAX44oXNNvLHGqAOcoVxmjZiohstwQ7SqKnbR47akdNi+uleWD8+g6A== @@ -4407,6 +4407,13 @@ csstype@^3.0.2: resolved "https://registry.yarnpkg.com/csstype/-/csstype-3.1.3.tgz#d80ff294d114fb0e6ac500fbf85b60137d7eff81" integrity sha512-M1uQkMl8rQK/szD0LNhtqxIPLpimGm8sOBwU7lLnCpSbTyY3yeU1Vc7l4KT5zT4s/yOxHH5O7tIuuLOCnLADRw== +d3-array@2, d3-array@^2.3.0, d3-array@^2.5.0: + version "2.12.1" + resolved "https://registry.yarnpkg.com/d3-array/-/d3-array-2.12.1.tgz#e20b41aafcdffdf5d50928004ececf815a465e81" + integrity sha512-B0ErZK/66mHtEsR1TkPEEkwdy+WDesimkM5gpZr5Dsg54BiTA5RXtYW5qTLIAcekaS9xfZrzBLF/OAkB3Qn1YQ== + dependencies: + internmap "^1.0.0" + "d3-array@2 - 3", "d3-array@2.10.0 - 3", "d3-array@2.5.0 - 3", d3-array@3, d3-array@^3.1.6, d3-array@^3.2.0: version "3.2.4" resolved "https://registry.yarnpkg.com/d3-array/-/d3-array-3.2.4.tgz#15fec33b237f97ac5d7c986dc77da273a8ed0bb5" @@ -4437,6 +4444,23 @@ d3-chord@3: dependencies: d3-path "1 - 3" +d3-cloud@^1.2.5: + version "1.2.7" + resolved "https://registry.yarnpkg.com/d3-cloud/-/d3-cloud-1.2.7.tgz#5a733c4bae43238cbb4760bb8f2d15912a8ad7a5" + integrity sha512-8TrgcgwRIpoZYQp7s3fGB7tATWfhckRb8KcVd1bOgqkNdkJRDGWfdSf4HkHHzZxSczwQJdSxvfPudwir5IAJ3w== + dependencies: + d3-dispatch "^1.0.3" + +d3-color@1: + version "1.4.1" + resolved "https://registry.yarnpkg.com/d3-color/-/d3-color-1.4.1.tgz#c52002bf8846ada4424d55d97982fef26eb3bc8a" + integrity sha512-p2sTHSLCJI2QKunbGb7ocOh7DgTAn8IrLx21QRc/BSnodXM4sv6aLQlnfpvehFMLZEfBc6g9pH9SWQccFYfJ9Q== + +"d3-color@1 - 2": + version "2.0.0" + resolved "https://registry.yarnpkg.com/d3-color/-/d3-color-2.0.0.tgz#8d625cab42ed9b8f601a1760a389f7ea9189d62e" + integrity sha512-SPXi0TSKPD4g9tw0NMZFnR95XVgUZiBH+uUTqQuDu1OsE2zomHU7ho0FISciaPvosimixwHFl3WHLGabv6dDgQ== + "d3-color@1 - 3", d3-color@3: version "3.1.0" resolved "https://registry.yarnpkg.com/d3-color/-/d3-color-3.1.0.tgz#395b2833dfac71507f12ac2f7af23bf819de24e2" @@ -4456,6 +4480,11 @@ d3-delaunay@6: dependencies: delaunator "5" +d3-dispatch@1, d3-dispatch@^1.0.3, d3-dispatch@^1.0.6: + version "1.0.6" + resolved "https://registry.yarnpkg.com/d3-dispatch/-/d3-dispatch-1.0.6.tgz#00d37bcee4dd8cd97729dd893a0ac29caaba5d58" + integrity sha512-fVjoElzjhCEy+Hbn8KygnmMS7Or0a9sI2UzGwoB7cCtvI1XpVN9GpoYlnb3xt2YV66oXYb1fLJ8GMvP4hdU1RA== + "d3-dispatch@1 - 3", d3-dispatch@3: version "3.0.1" resolved "https://registry.yarnpkg.com/d3-dispatch/-/d3-dispatch-3.0.1.tgz#5fc75284e9c2375c36c839411a0cf550cbfc4d5e" @@ -4478,6 +4507,11 @@ d3-delaunay@6: iconv-lite "0.6" rw "1" +d3-ease@1: + version "1.0.7" + resolved "https://registry.yarnpkg.com/d3-ease/-/d3-ease-1.0.7.tgz#9a834890ef8b8ae8c558b2fe55bd57f5993b85e2" + integrity sha512-lx14ZPYkhNx0s/2HX5sLFUI3mbasHjSSpwO/KaaNACweVwxUruKyWVcb293wMv1RqTPZyZ8kSZ2NogUZNcLOFQ== + "d3-ease@1 - 3", d3-ease@3, d3-ease@^3.0.1: version "3.0.1" resolved "https://registry.yarnpkg.com/d3-ease/-/d3-ease-3.0.1.tgz#9658ac38a2140d59d346160f1f6c30fda0bd12f4" @@ -4499,6 +4533,11 @@ d3-force@3: d3-quadtree "1 - 3" d3-timer "1 - 3" +"d3-format@1 - 2": + version "2.0.0" + resolved "https://registry.yarnpkg.com/d3-format/-/d3-format-2.0.0.tgz#a10bcc0f986c372b729ba447382413aabf5b0767" + integrity sha512-Ab3S6XuE/Q+flY96HXT0jOXcM4EAClYFnRGY5zsjRGNy6qCYrQsMffs7cV5Q9xejb35zxW5hf/guKw34kvIKsA== + "d3-format@1 - 3", d3-format@3: version "3.1.0" resolved "https://registry.yarnpkg.com/d3-format/-/d3-format-3.1.0.tgz#9260e23a28ea5cb109e93b21a06e24e2ebd55641" @@ -4516,6 +4555,13 @@ d3-hierarchy@3: resolved "https://registry.yarnpkg.com/d3-hierarchy/-/d3-hierarchy-3.1.2.tgz#b01cd42c1eed3d46db77a5966cf726f8c09160c6" integrity sha512-FX/9frcub54beBdugHjDCdikxThEqjnR93Qt7PvQTOHxyiNCAlvMrHhclk3cD5VeAaq9fxmfRp+CnWw9rEMBuA== +d3-interpolate@1: + version "1.4.0" + resolved "https://registry.yarnpkg.com/d3-interpolate/-/d3-interpolate-1.4.0.tgz#526e79e2d80daa383f9e0c1c1c7dcc0f0583e987" + integrity sha512-V9znK0zc3jOPV4VD2zZn0sDhZU3WAE2bmlxdIwwQPPzPjvyLkd8B3JUVdS1IDUFDkWZ72c9qnv1GK2ZagTZ8EA== + dependencies: + d3-color "1" + "d3-interpolate@1 - 3", "d3-interpolate@1.2.0 - 3", d3-interpolate@3, d3-interpolate@^3.0.1: version "3.0.1" resolved "https://registry.yarnpkg.com/d3-interpolate/-/d3-interpolate-3.0.1.tgz#3c47aa5b32c5b3dfb56ef3fd4342078a632b400d" @@ -4523,6 +4569,13 @@ d3-hierarchy@3: dependencies: d3-color "1 - 3" +"d3-interpolate@1.2.0 - 2": + version "2.0.1" + resolved "https://registry.yarnpkg.com/d3-interpolate/-/d3-interpolate-2.0.1.tgz#98be499cfb8a3b94d4ff616900501a64abc91163" + integrity sha512-c5UhwwTs/yybcmTpAVqwSFl6vrQ8JZJoT5F7xNFK9pymv5C0Ymcc9/LIJHtYIggg/yS9YHw8i8O8tgb9pupjeQ== + dependencies: + d3-color "1 - 2" + "d3-path@1 - 3", d3-path@3, d3-path@^3.1.0: version "3.1.0" resolved "https://registry.yarnpkg.com/d3-path/-/d3-path-3.1.0.tgz#22df939032fb5a71ae8b1800d61ddb7851c42526" @@ -4551,6 +4604,14 @@ d3-scale-chromatic@3: d3-color "1 - 3" d3-interpolate "1 - 3" +d3-scale-chromatic@^1.5.0: + version "1.5.0" + resolved "https://registry.yarnpkg.com/d3-scale-chromatic/-/d3-scale-chromatic-1.5.0.tgz#54e333fc78212f439b14641fb55801dd81135a98" + integrity sha512-ACcL46DYImpRFMBcpk9HhtIyC7bTBR4fNOPxwVSl0LfulDAwyiHyPOTqcDG1+t5d4P9W7t/2NAuWu59aKko/cg== + dependencies: + d3-color "1" + d3-interpolate "1" + d3-scale@4, d3-scale@^4.0.2: version "4.0.2" resolved "https://registry.yarnpkg.com/d3-scale/-/d3-scale-4.0.2.tgz#82b38e8e8ff7080764f8dcec77bd4be393689396" @@ -4562,6 +4623,22 @@ d3-scale@4, d3-scale@^4.0.2: d3-time "2.1.1 - 3" d3-time-format "2 - 4" +d3-scale@^3.2.1: + version "3.3.0" + resolved "https://registry.yarnpkg.com/d3-scale/-/d3-scale-3.3.0.tgz#28c600b29f47e5b9cd2df9749c206727966203f3" + integrity sha512-1JGp44NQCt5d1g+Yy+GeOnZP7xHo0ii8zsQp6PGzd+C1/dl0KGsp9A7Mxwp+1D1o4unbTTxVdU/ZOIEBoeZPbQ== + dependencies: + d3-array "^2.3.0" + d3-format "1 - 2" + d3-interpolate "1.2.0 - 2" + d3-time "^2.1.1" + d3-time-format "2 - 3" + +d3-selection@1.4.2, d3-selection@^1.1.0: + version "1.4.2" + resolved "https://registry.yarnpkg.com/d3-selection/-/d3-selection-1.4.2.tgz#dcaa49522c0dbf32d6c1858afc26b6094555bc5c" + integrity sha512-SJ0BqYihzOjDnnlfyeHT0e30k0K1+5sR3d5fNueCNeuhZTnGw4M4o8mqJchSwgKMXCNFo+e2VTChiSJ0vYtXkg== + "d3-selection@2 - 3", d3-selection@3: version "3.0.0" resolved "https://registry.yarnpkg.com/d3-selection/-/d3-selection-3.0.0.tgz#c25338207efa72cc5b9bd1458a1a41901f1e1b31" @@ -4574,6 +4651,13 @@ d3-shape@3, d3-shape@^3.1.0: dependencies: d3-path "^3.1.0" +"d3-time-format@2 - 3": + version "3.0.0" + resolved "https://registry.yarnpkg.com/d3-time-format/-/d3-time-format-3.0.0.tgz#df8056c83659e01f20ac5da5fdeae7c08d5f1bb6" + integrity 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"1.0.10" + resolved "https://registry.yarnpkg.com/d3-timer/-/d3-timer-1.0.10.tgz#dfe76b8a91748831b13b6d9c793ffbd508dd9de5" + integrity sha512-B1JDm0XDaQC+uvo4DT79H0XmBskgS3l6Ve+1SBCfxgmtIb1AVrPIoqd+nPSv+loMX8szQ0sVUhGngL7D5QPiXw== + "d3-timer@1 - 3", d3-timer@3, d3-timer@^3.0.1: version "3.0.1" resolved "https://registry.yarnpkg.com/d3-timer/-/d3-timer-3.0.1.tgz#6284d2a2708285b1abb7e201eda4380af35e63b0" @@ -4604,6 +4700,18 @@ d3-shape@3, d3-shape@^3.1.0: d3-interpolate "1 - 3" d3-timer "1 - 3" +d3-transition@^1.3.2: + version "1.3.2" + resolved "https://registry.yarnpkg.com/d3-transition/-/d3-transition-1.3.2.tgz#a98ef2151be8d8600543434c1ca80140ae23b398" + integrity sha512-sc0gRU4PFqZ47lPVHloMn9tlPcv8jxgOQg+0zjhfZXMQuvppjG6YuwdMBE0TuqCZjeJkLecku/l9R0JPcRhaDA== + dependencies: + d3-color "1" + d3-dispatch "1" + d3-ease "1" + d3-interpolate "1" + d3-selection "^1.1.0" + d3-timer "1" + d3-voronoi@^1.1.4: version "1.1.4" resolved "https://registry.yarnpkg.com/d3-voronoi/-/d3-voronoi-1.1.4.tgz#dd3c78d7653d2bb359284ae478645d95944c8297" @@ -6674,6 +6782,11 @@ internal-slot@^1.0.4, internal-slot@^1.0.7: resolved "https://registry.yarnpkg.com/internmap/-/internmap-2.0.3.tgz#6685f23755e43c524e251d29cbc97248e3061009" integrity sha512-5Hh7Y1wQbvY5ooGgPbDaL5iYLAPzMTUrjMulskHLH6wnv/A+1q5rgEaiuqEjB+oxGXIVZs1FF+R/KPN3ZSQYYg== +internmap@^1.0.0: + version "1.0.1" + resolved "https://registry.yarnpkg.com/internmap/-/internmap-1.0.1.tgz#0017cc8a3b99605f0302f2b198d272e015e5df95" + integrity sha512-lDB5YccMydFBtasVtxnZ3MRBHuaoE8GKsppq+EchKL2U4nK/DmEpPHNH8MZe5HkMtpSiTSOZwfN0tzYjO/lJEw== + invariant@^2.2.1, invariant@^2.2.4: version "2.2.4" resolved "https://registry.yarnpkg.com/invariant/-/invariant-2.2.4.tgz#610f3c92c9359ce1db616e538008d23ff35158e6" @@ -7844,6 +7957,11 @@ locate-path@^6.0.0: dependencies: p-locate "^5.0.0" +lodash.clonedeep@^4.5.0: + version "4.5.0" + resolved "https://registry.yarnpkg.com/lodash.clonedeep/-/lodash.clonedeep-4.5.0.tgz#e23f3f9c4f8fbdde872529c1071857a086e5ccef" + integrity sha512-H5ZhCF25riFd9uB5UCkVKo61m3S/xZk1x4wA6yp/L3RFP6Z/eHH1ymQcGLo7J3GMPfm0V/7m1tryHuGVxpqEBQ== + lodash.debounce@^4.0.8: version "4.0.8" resolved "https://registry.yarnpkg.com/lodash.debounce/-/lodash.debounce-4.0.8.tgz#82d79bff30a67c4005ffd5e2515300ad9ca4d7af" @@ -9731,6 +9849,24 @@ react-tooltip@^5.11.2: "@floating-ui/dom" "^1.6.1" classnames "^2.3.0" +react-wordcloud@^1.2.7: + version "1.2.7" + resolved "https://registry.yarnpkg.com/react-wordcloud/-/react-wordcloud-1.2.7.tgz#6a21d9a64a8f9b0f7d12eef789156538794e685c" + integrity sha512-pyXvL8Iu2J258Qk2/kAwY23dIVhNpMC3dnvbXRkw5+Ert5EkJWwnwVjs9q8CmX38NWbfCKhGmpjuumBoQEtniw== + dependencies: + d3-array "^2.5.0" + d3-cloud "^1.2.5" + d3-dispatch "^1.0.6" + d3-scale "^3.2.1" + d3-scale-chromatic "^1.5.0" + d3-selection "1.4.2" + d3-transition "^1.3.2" + lodash.clonedeep "^4.5.0" + lodash.debounce "^4.0.8" + resize-observer-polyfill "^1.5.1" + seedrandom "^3.0.5" + tippy.js "^6.2.6" + react@17.0.1: version "17.0.1" resolved "https://registry.yarnpkg.com/react/-/react-17.0.1.tgz#6e0600416bd57574e3f86d92edba3d9008726127" @@ -9912,6 +10048,11 @@ requires-port@^1.0.0: resolved "https://registry.yarnpkg.com/requires-port/-/requires-port-1.0.0.tgz#925d2601d39ac485e091cf0da5c6e694dc3dcaff" integrity sha512-KigOCHcocU3XODJxsu8i/j8T9tzT4adHiecwORRQ0ZZFcp7ahwXuRU1m+yuO90C5ZUyGeGfocHDI14M3L3yDAQ== +resize-observer-polyfill@^1.5.1: + version "1.5.1" + resolved "https://registry.yarnpkg.com/resize-observer-polyfill/-/resize-observer-polyfill-1.5.1.tgz#0e9020dd3d21024458d4ebd27e23e40269810464" + integrity sha512-LwZrotdHOo12nQuZlHEmtuXdqGoOD0OhaxopaNFxWzInpEgaLWoVuAMbTzixuosCx2nEG58ngzW3vxdWoxIgdg== + resolve-cwd@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/resolve-cwd/-/resolve-cwd-3.0.0.tgz#0f0075f1bb2544766cf73ba6a6e2adfebcb13f2d" @@ -10152,6 +10293,11 @@ scroll-into-view-if-needed@^3.1.0: dependencies: compute-scroll-into-view "^3.0.2" +seedrandom@^3.0.5: + version "3.0.5" + resolved "https://registry.yarnpkg.com/seedrandom/-/seedrandom-3.0.5.tgz#54edc85c95222525b0c7a6f6b3543d8e0b3aa0a7" + integrity sha512-8OwmbklUNzwezjGInmZ+2clQmExQPvomqjL7LFqOYqtmuxRgQYqOD3mHaU+MvZn5FLUeVxVfQjwLZW/n/JFuqg== + select-hose@^2.0.0: version "2.0.0" resolved "https://registry.yarnpkg.com/select-hose/-/select-hose-2.0.0.tgz#625d8658f865af43ec962bfc376a37359a4994ca" @@ -10489,7 +10635,16 @@ string-natural-compare@^3.0.1: resolved "https://registry.yarnpkg.com/string-natural-compare/-/string-natural-compare-3.0.1.tgz#7a42d58474454963759e8e8b7ae63d71c1e7fdf4" integrity sha512-n3sPwynL1nwKi3WJ6AIsClwBMa0zTi54fn2oLU6ndfTSIO05xaznjSf15PcBZU6FNWbmN5Q6cxT4V5hGvB4taw== -"string-width-cjs@npm:string-width@^4.2.0", string-width@^4.1.0, string-width@^4.2.0, string-width@^4.2.3: +"string-width-cjs@npm:string-width@^4.2.0": + version "4.2.3" + resolved "https://registry.yarnpkg.com/string-width/-/string-width-4.2.3.tgz#269c7117d27b05ad2e536830a8ec895ef9c6d010" + integrity sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g== + dependencies: + emoji-regex "^8.0.0" + is-fullwidth-code-point "^3.0.0" + strip-ansi "^6.0.1" + +string-width@^4.1.0, string-width@^4.2.0, string-width@^4.2.3: version "4.2.3" resolved "https://registry.yarnpkg.com/string-width/-/string-width-4.2.3.tgz#269c7117d27b05ad2e536830a8ec895ef9c6d010" integrity sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g== @@ -10584,7 +10739,14 @@ stringify-object@^3.3.0: is-obj "^1.0.1" is-regexp "^1.0.0" -"strip-ansi-cjs@npm:strip-ansi@^6.0.1", strip-ansi@^6.0.0, strip-ansi@^6.0.1: +"strip-ansi-cjs@npm:strip-ansi@^6.0.1": + version "6.0.1" + resolved "https://registry.yarnpkg.com/strip-ansi/-/strip-ansi-6.0.1.tgz#9e26c63d30f53443e9489495b2105d37b67a85d9" + integrity sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A== + dependencies: + ansi-regex "^5.0.1" + +strip-ansi@^6.0.0, strip-ansi@^6.0.1: version "6.0.1" resolved "https://registry.yarnpkg.com/strip-ansi/-/strip-ansi-6.0.1.tgz#9e26c63d30f53443e9489495b2105d37b67a85d9" integrity sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A== @@ -10969,6 +11131,13 @@ tiny-warning@^1.0.0: resolved "https://registry.yarnpkg.com/tiny-warning/-/tiny-warning-1.0.3.tgz#94a30db453df4c643d0fd566060d60a875d84754" integrity sha512-lBN9zLN/oAf68o3zNXYrdCt1kP8WsiGW8Oo2ka41b2IM5JL/S1CTyX1rW0mb/zSuJun0ZUrDxx4sqvYS2FWzPA== +tippy.js@^6.2.6: + version "6.3.7" + resolved "https://registry.yarnpkg.com/tippy.js/-/tippy.js-6.3.7.tgz#8ccfb651d642010ed9a32ff29b0e9e19c5b8c61c" + integrity sha512-E1d3oP2emgJ9dRQZdf3Kkn0qJgI6ZLpyS5z6ZkY1DF3kaQaBsGZsndEpHwx+eC+tYM41HaSNvNtLx8tU57FzTQ== + dependencies: + "@popperjs/core" "^2.9.0" + tmpl@1.0.5: version "1.0.5" resolved "https://registry.yarnpkg.com/tmpl/-/tmpl-1.0.5.tgz#8683e0b902bb9c20c4f726e3c0b69f36518c07cc" @@ -12161,7 +12330,16 @@ workbox-window@6.6.1: "@types/trusted-types" "^2.0.2" workbox-core "6.6.1" -"wrap-ansi-cjs@npm:wrap-ansi@^7.0.0", wrap-ansi@^7.0.0: +"wrap-ansi-cjs@npm:wrap-ansi@^7.0.0": + version "7.0.0" + resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-7.0.0.tgz#67e145cff510a6a6984bdf1152911d69d2eb9e43" + integrity sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q== + dependencies: + ansi-styles "^4.0.0" + string-width "^4.1.0" + strip-ansi "^6.0.0" + +wrap-ansi@^7.0.0: version "7.0.0" resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-7.0.0.tgz#67e145cff510a6a6984bdf1152911d69d2eb9e43" integrity sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q== From b012debcd82508b8dcd7e203af7b24b4682036cf Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Fri, 1 Nov 2024 10:37:00 -0700 Subject: [PATCH 02/31] Rename component to 'ProjectOverview' --- src/MainStudy/{mainStudy.jsx => overview.jsx} | 21 +++++++++++-------- 1 file changed, 12 insertions(+), 9 deletions(-) rename src/MainStudy/{mainStudy.jsx => overview.jsx} (95%) diff --git a/src/MainStudy/mainStudy.jsx b/src/MainStudy/overview.jsx similarity index 95% rename from src/MainStudy/mainStudy.jsx rename to src/MainStudy/overview.jsx index 872d4905..4f298aa3 100644 --- a/src/MainStudy/mainStudy.jsx +++ b/src/MainStudy/overview.jsx @@ -10,7 +10,7 @@ import PASS1B06Profiling from '../assets/figures/pass1b-06-molecular-profiling.s import ToggleShowHide from './components/toggleShowHide'; import ExternalLink from '../lib/ui/externalLink'; -function MainStudy({ profile, allFiles, handleDataFetch }) { +function ProjectOverview({ profile, allFiles, handleDataFetch }) { const [showSummary, setShowSummary] = useState(true); const [showExpDesign, setShowExpDesign] = useState(true); const [showTissueProfiling, setShowTissueProfiling] = useState(true); @@ -166,7 +166,9 @@ function MainStudy({ profile, allFiles, handleDataFetch }) { >

Endurance Training in Young Adult Rats

- Species: Rattus norvegicus + Species: + {' '} + Rattus norvegicus

In this intervention, we're specifically interested in the long term @@ -176,11 +178,13 @@ function MainStudy({ profile, allFiles, handleDataFetch }) { tissues. Rats were endurance-exercise trained on treadmills and tissue samples were collected at either 1, 2, 4, or 8 weeks of training, with a 48 hour rest or wash out period before samples were - collected. See the{' '} + collected. See the + {' '} {' '} + /> + {' '} to learn more.

@@ -257,7 +261,7 @@ function MainStudy({ profile, allFiles, handleDataFetch }) { ); } -MainStudy.propTypes = { +ProjectOverview.propTypes = { profile: PropTypes.shape({ user_metadata: PropTypes.shape({ hasAccess: PropTypes.bool, @@ -267,7 +271,7 @@ MainStudy.propTypes = { handleDataFetch: PropTypes.func, }; -MainStudy.defaultProps = { +ProjectOverview.defaultProps = { profile: {}, handleDataFetch: null, }; @@ -277,8 +281,7 @@ const mapStateToProps = (state) => ({ }); const mapDispatchToProps = (dispatch) => ({ - handleDataFetch: (phase) => - dispatch(BrowseDataActions.handleDataFetch(phase)), + handleDataFetch: (phase) => dispatch(BrowseDataActions.handleDataFetch(phase)), }); -export default connect(mapStateToProps, mapDispatchToProps)(MainStudy); +export default connect(mapStateToProps, mapDispatchToProps)(ProjectOverview); From cac383d7244c98fc31b064f6ab0bb3f913319ae7 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Fri, 1 Nov 2024 10:38:06 -0700 Subject: [PATCH 03/31] Add new ExerciseBenefits component and app route --- src/App/App.jsx | 9 +- src/MainStudy/exerciseBenefits.jsx | 130 +++++++++++++++++++++++++++++ 2 files changed, 137 insertions(+), 2 deletions(-) create mode 100644 src/MainStudy/exerciseBenefits.jsx diff --git a/src/App/App.jsx b/src/App/App.jsx index d83cd4eb..0eb5c7fb 100644 --- a/src/App/App.jsx +++ b/src/App/App.jsx @@ -25,7 +25,8 @@ import SearchPageConnected from '../Search/searchPage'; import GeneCentricViewConnected from '../AnalysisPage/GeneCentricViewRat/geneCentricViewPage'; import GraphicalClustering from '../AnalysisPage/GraphicalClustering/graphicalClusteringPage'; import CodeRepositories from '../CodeRepoPage/codeRepoPage'; -import MainStudyConnected from '../MainStudy/mainStudy'; +import ProjectOverviewConnected from '../MainStudy/overview'; +import ExerciseBenefits from '../MainStudy/exerciseBenefits'; import Tutorials from '../Tutorials/tutorials'; import Publications from '../Publications/publications'; import MultiOmicsWorkingGroups from '../MultiOmicsWorkingGroups/multiOmicsWorkingGroups'; @@ -134,7 +135,11 @@ function App({ history = History }) { /> + ({ + text: benefit, + value: getRandomInt(100, 800), + })); + + return ( +
+ + + Benefits of Exercise - MoTrPAC Data Hub + + +
+
+
+

+ Regular physical activity is associated with many health benefits, + supported by extensive evidence in the medical literature. +

+
+
+ +
+
+
+ + + + + + + + + {exerciseBenefitList.map((benefit) => ( + + + + + ))} + +
Health BenefitEvidence
{benefit.title}{benefit.evidence}
+
+
+
+ ); +} + +export default ExerciseBenefits; From aa0c64fcc18bbf545bc024038d85415a45346272 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Fri, 1 Nov 2024 10:39:41 -0700 Subject: [PATCH 04/31] Rename 'Help' top nav link to 'Learn' and add dropdown menu links to exercise benefits and study assays --- src/Navbar/navbar.jsx | 24 +++++++++++++++--------- 1 file changed, 15 insertions(+), 9 deletions(-) diff --git a/src/Navbar/navbar.jsx b/src/Navbar/navbar.jsx index 7bc7ea5b..2435fdde 100644 --- a/src/Navbar/navbar.jsx +++ b/src/Navbar/navbar.jsx @@ -345,7 +345,7 @@ export function Navbar({ id="helpNavbarItemMenuLink" data-toggle="dropdown" > - Help + Learn
Project Overview + + Exercise Benefits + + + Study Assays + Tutorials - checkServiceStatus(e)} - > - Contact Us -
  • @@ -389,6 +387,14 @@ export function Navbar({ Useful Links + checkServiceStatus(e)} + > + Contact Us +
    • From 5f46a7bfaa88819d62fcf2a192d4549fcc72fe30 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Fri, 1 Nov 2024 10:40:30 -0700 Subject: [PATCH 05/31] Add style to override react-wordcloud tooltip display --- src/sass/mainStudy/_mainStudyPage.scss | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/sass/mainStudy/_mainStudyPage.scss b/src/sass/mainStudy/_mainStudyPage.scss index 88d233c3..3c4b0b18 100644 --- a/src/sass/mainStudy/_mainStudyPage.scss +++ b/src/sass/mainStudy/_mainStudyPage.scss @@ -70,3 +70,8 @@ } } } + +// disable react-wordcloud tooltip +div[data-tippy-root=""] { + display: none !important; +} \ No newline at end of file From d63bd1cf82ab3ea78ec892d6ffd4bdea360547d3 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Mon, 4 Nov 2024 02:01:00 -0800 Subject: [PATCH 06/31] Add Highcharts dependency for visualizations --- package.json | 2 ++ yarn.lock | 10 ++++++++++ 2 files changed, 12 insertions(+) diff --git a/package.json b/package.json index e5ac6643..7246dd9a 100644 --- a/package.json +++ b/package.json @@ -13,6 +13,8 @@ "dayjs": "1.11.7", "from-exponential": "^1.1.1", "ga-gtag": "1.2.0", + "highcharts": "^11.4.8", + "highcharts-react-official": "^3.2.1", "history": "4.10.1", "http-proxy-middleware": "^2.0.1", "jquery": "^3.5.1", diff --git a/yarn.lock b/yarn.lock index 09170453..60d9d735 100644 --- a/yarn.lock +++ b/yarn.lock @@ -6475,6 +6475,16 @@ hexoid@^1.0.0: resolved "https://registry.yarnpkg.com/hexoid/-/hexoid-1.0.0.tgz#ad10c6573fb907de23d9ec63a711267d9dc9bc18" integrity sha512-QFLV0taWQOZtvIRIAdBChesmogZrtuXvVWsFHZTk2SU+anspqZ2vMnoLg7IE1+Uk16N19APic1BuF8bC8c2m5g== +highcharts-react-official@^3.2.1: + version "3.2.1" + resolved "https://registry.yarnpkg.com/highcharts-react-official/-/highcharts-react-official-3.2.1.tgz#4b62a7af2969bdebde6b338d36f6b9bf1f1029bc" + integrity sha512-hyQTX7ezCxl7JqumaWiGsroGWalzh24GedQIgO3vJbkGOZ6ySRAltIYjfxhrq4HszJOySZegotEF7v+haQ75UA== + +highcharts@^11.4.8: + version "11.4.8" + resolved "https://registry.yarnpkg.com/highcharts/-/highcharts-11.4.8.tgz#252e71b81c24ec9f99e756b76dbebd7546e18dda" + integrity sha512-5Tke9LuzZszC4osaFisxLIcw7xgNGz4Sy3Jc9pRMV+ydm6sYqsPYdU8ELOgpzGNrbrRNDRBtveoR5xS3SzneEA== + history@4.10.1, history@^4.9.0: version "4.10.1" resolved "https://registry.yarnpkg.com/history/-/history-4.10.1.tgz#33371a65e3a83b267434e2b3f3b1b4c58aad4cf3" From 6e8e90f874919b75647536faad4b93dd7a7f4730 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Mon, 4 Nov 2024 02:01:47 -0800 Subject: [PATCH 07/31] Add route for pass1b-06 study assay-tissue visualization --- src/App/App.jsx | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/App/App.jsx b/src/App/App.jsx index 0eb5c7fb..f32861fe 100644 --- a/src/App/App.jsx +++ b/src/App/App.jsx @@ -27,6 +27,7 @@ import GraphicalClustering from '../AnalysisPage/GraphicalClustering/graphicalCl import CodeRepositories from '../CodeRepoPage/codeRepoPage'; import ProjectOverviewConnected from '../MainStudy/overview'; import ExerciseBenefits from '../MainStudy/exerciseBenefits'; +import StudyAssays from '../MainStudy/studyAssays'; import Tutorials from '../Tutorials/tutorials'; import Publications from '../Publications/publications'; import MultiOmicsWorkingGroups from '../MultiOmicsWorkingGroups/multiOmicsWorkingGroups'; @@ -141,6 +142,10 @@ function App({ history = History }) { path="/exercise-benefits" component={withTracker(ExerciseBenefits)} /> + Date: Mon, 4 Nov 2024 02:05:14 -0800 Subject: [PATCH 08/31] Move exercise benefit list to external file; add citation anchor links to benefit evidence; add display of references --- src/MainStudy/exerciseBenefits.jsx | 83 +++++++++++++++++------------- 1 file changed, 48 insertions(+), 35 deletions(-) diff --git a/src/MainStudy/exerciseBenefits.jsx b/src/MainStudy/exerciseBenefits.jsx index 445bede6..81c26d5f 100644 --- a/src/MainStudy/exerciseBenefits.jsx +++ b/src/MainStudy/exerciseBenefits.jsx @@ -4,6 +4,8 @@ import { Helmet } from 'react-helmet'; import ReactWordcloud from 'react-wordcloud'; import PageTitle from '../lib/ui/pageTitle'; import ExternalLink from '../lib/ui/externalLink'; +import exerciseBenefitsData from './exerciseBenefitsData'; +import exerciseBenefitsReferenceData from './exerciseBenefitsReferenceData'; const exerciseBenefits = [ 'Improved immune system', @@ -22,43 +24,12 @@ const exerciseBenefits = [ 'Increased reliance on lipid metabolism', 'Stronger skeleton, joints and tendons', 'Reduced risk of all-cause mortality', - 'Reduced risk of cardiovascular disease', + 'Reduced risk of cardiovascular diseases', 'Improved cognition', 'Reduced stress response', 'Reduced risk for dementia', ]; -const exerciseBenefitList = [ - { - title: 'Younger-looking skin', - evidence: 'Exercise improves skin health by enhancing blood flow and delivering oxygen and nutrients to the skin, promoting collagen production and reducing signs of aging.', - }, - { - title: 'Reduced risk of cancer', - evidence: 'Physical activity is linked to a lower risk of several cancers, including colon, breast, and prostate. The American College of Sports Medicine notes that exercise decreases the risk of developing these cancers.', - }, - { - title: 'Reduced risk of metabolic disease', - evidence: 'Regular exercise improves insulin sensitivity, reduces the risk of type 2 diabetes, and enhances overall metabolic health.', - }, - { - title: 'Better temperature regulation', - evidence: 'Exercise improves thermoregulation by enhancing sweat response and increasing blood flow to the skin.', - }, - { - title: 'Better sex', - evidence: 'Physical activity is associated with improved sexual function and satisfaction, likely due to enhanced cardiovascular health and psychological well-being.', - }, - { - title: 'Improved sleep', - evidence: 'Exercise has been shown to improve sleep quality and reduce the time it takes to fall asleep.', - }, - { - title: 'Reduced risk for depression', - evidence: 'Regular physical activity reduces the risk of depression and anxiety, as highlighted by the United States Department of Health and Human Services.', - }, -]; - function ExerciseBenefits() { const options = { rotations: 0, @@ -113,14 +84,56 @@ function ExerciseBenefits() { - {exerciseBenefitList.map((benefit) => ( - + {exerciseBenefitsData.map((benefit) => ( + {benefit.title} - {benefit.evidence} + + {benefit.evidence} + + [ + + {benefit.citationNo} + + ] + + ))} +

    + These benefits underscore the importance of regular physical activity + as a cornerstone of preventive health care. +

    + +
    +
    +
    + References: +
    +
      + {exerciseBenefitsReferenceData.map((reference) => ( +
    1. +

      + {reference.title} +
      + {`${reference.author}.`} +
      + {`${reference.journal}.`} + {' '} + {`${reference.publicationIssue}.`} +
      + doi: + {' '} + +

      +
      2. + ))} +
    +
    From 08e5720e63e20c4db43d4c00523f6710249642ee Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Mon, 4 Nov 2024 02:06:30 -0800 Subject: [PATCH 09/31] Initial commit of exercise benefits data as external file --- src/MainStudy/exerciseBenefitsData.js | 104 ++++++++++++++++++++++++++ 1 file changed, 104 insertions(+) create mode 100644 src/MainStudy/exerciseBenefitsData.js diff --git a/src/MainStudy/exerciseBenefitsData.js b/src/MainStudy/exerciseBenefitsData.js new file mode 100644 index 00000000..3a4c297c --- /dev/null +++ b/src/MainStudy/exerciseBenefitsData.js @@ -0,0 +1,104 @@ +const exerciseBenefitsData = [ + { + title: 'Younger-looking skin', + evidence: 'Exercise improves skin health by enhancing blood flow and delivering oxygen and nutrients to the skin, promoting collagen production and reducing signs of aging.', + citationNo: 1, + }, + { + title: 'Reduced risk of cancer', + evidence: 'Physical activity is linked to a lower risk of several cancers, including colon, breast, and prostate. The American College of Sports Medicine notes that exercise decreases the risk of developing these cancers.', + citationNo: 2, + }, + { + title: 'Reduced risk of metabolic disease', + evidence: 'Regular exercise improves insulin sensitivity, reduces the risk of type 2 diabetes, and enhances overall metabolic health.', + citationNo: 3, + }, + { + title: 'Better temperature regulation', + evidence: 'Exercise improves thermoregulation by enhancing sweat response and increasing blood flow to the skin.', + citationNo: 1, + }, + { + title: 'Better sex', + evidence: 'Physical activity is associated with improved sexual function and satisfaction, likely due to enhanced cardiovascular health and psychological well-being.', + citationNo: 1, + }, + { + title: 'Improved sleep', + evidence: 'Exercise has been shown to improve sleep quality and reduce the time it takes to fall asleep.', + citationNo: 4, + }, + { + title: 'Reduced risk for depression', + evidence: 'Regular physical activity reduces the risk of depression and anxiety, as highlighted by the United States Department of Health and Human Services.', + citationNo: 4, + }, + { + title: 'Improved insulin sensitivity', + evidence: 'Exercise enhances insulin sensitivity, reducing the risk of insulin resistance and type 2 diabetes.', + citationNo: 3, + }, + { + title: 'Improved blood lipid profile', + evidence: 'Physical activity improves lipid profiles by increasing HDL cholesterol and reducing LDL cholesterol and triglycerides.', + citationNo: 5, + }, + { + title: 'Better self-esteem', + evidence: 'Regular exercise is associated with improved self-esteem and overall psychological well-being.', + citationNo: 1, + }, + { + title: 'Better oxygen transport', + evidence: 'Exercise increases erythrocyte count, promotes angiogenesis, and strengthens the heart, enhancing oxygen transport and cardiovascular efficiency.', + citationNo: 5, + }, + { + title: 'More, larger, and more efficient mitochondria', + evidence: 'Exercise promotes mitochondrial biogenesis and efficiency, crucial for metabolic health.', + citationNo: 6, + }, + { + title: 'Increased reliance on lipid metabolism', + evidence: 'Regular physical activity enhances the body\'s ability to utilize lipids for energy, improving metabolic flexibility.', + citationNo: 3, + }, + { + title: 'Stronger skeleton, joints, and tendons', + evidence: 'Weight-bearing and resistance exercises improve bone density and joint health, reducing the risk of osteoporosis and fractures.', + citationNo: 2, + }, + { + title: 'Reduced risk of all-cause mortality', + evidence: 'Regular physical activity is associated with a lower risk of all-cause mortality.', + citationNo: 4, + }, + { + title: 'Reduced risk of cardiovascular diseases', + evidence: 'Exercise reduces the risk of cardiovascular diseases, including heart disease and stroke.', + citationNo: 4, + }, + { + title: 'Improved cognition', + evidence: 'Physical activity is linked to better cognitive function and a reduced risk of cognitive decline and dementia.', + citationNo: 4, + }, + { + title: 'Reduced stress response', + evidence: 'Exercise helps modulate the body\'s stress response, reducing levels of stress hormones like cortisol.', + citationNo: 1, + }, + { + title: 'Reduced risk for dementia', + evidence: 'Regular physical activity is associated with a lower risk of developing dementia, including Alzheimer\'s disease.', + citationNo: 4, + }, + { + title: 'Positive effect on treatment of at least 26 different diseases', + evidence: 'Exercise has demonstrated therapeutic effects on 26 chronic diseases.', + citationNo: 7, + }, +]; + +export default exerciseBenefitsData; From 4cc3796b9f40b52ef290f1c549b9fbe85fba0a3e Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Mon, 4 Nov 2024 02:06:52 -0800 Subject: [PATCH 10/31] Initial commit of exercise benefits reference data as external file --- .../exerciseBenefitsReferenceData.js | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 src/MainStudy/exerciseBenefitsReferenceData.js diff --git a/src/MainStudy/exerciseBenefitsReferenceData.js b/src/MainStudy/exerciseBenefitsReferenceData.js new file mode 100644 index 00000000..ece587d5 --- /dev/null +++ b/src/MainStudy/exerciseBenefitsReferenceData.js @@ -0,0 +1,60 @@ +const exerciseBenefitsReferenceData = [ + { + citationNo: 1, + title: 'An Overview of the Beneficial Effects of Exercise on Health and Performance', + author: 'Kramer A', + journal: 'Advances in Experimental Medicine and Biology', + publicationIssue: '2020;1228:3-22', + doi: '10.1007/978-981-15-1792-1_1', + }, + { + citationNo: 2, + title: 'American College of Sports Medicine Position Stand. Quantity and Quality of Exercise for Developing and Maintaining Cardiorespiratory, Musculoskeletal, and Neuromotor Fitness in Apparently Healthy Adults: Guidance for Prescribing Exercise', + author: 'Garber CE, Blissmer B, Deschenes MR, et al', + journal: 'Medicine and Science in Sports and Exercise', + publicationIssue: '2011;43(7):1334-59', + doi: '10.1249/MSS.0b013e318213fefb', + }, + { + citationNo: 3, + title: 'Exercise and Metabolic Health: Beyond Skeletal Muscle', + author: 'Thyfault JP, Bergouignan A', + journal: 'Diabetologia', + publicationIssue: '2020;63(8):1464-1474', + doi: '10.1007/s00125-020-05177-6', + }, + { + citationNo: 4, + title: 'The Physical Activity Guidelines for Americans', + author: 'Piercy KL, Troiano RP, Ballard RM, et al', + journal: 'Jama', + publicationIssue: '2018;320(19):2020-2028', + doi: '10.1001/jama.2018.14854', + }, + { + citationNo: 5, + title: 'Statement on Exercise: Benefits and Recommendations for Physical Activity Programs for All Americans. A Statement for Health Professionals by the Committee on Exercise and Cardiac Rehabilitation of the Council on Clinical Cardiology, American Heart Association', + author: 'Fletcher GF, Balady G, Blair SN, et al', + journal: 'Circulation', + publicationIssue: '1996;94(4):857-62', + doi: '10.1161/01.cir.94.4.857', + }, + { + citationNo: 6, + title: 'Exercise Mitigates Age-Related Metabolic Diseases by Improving Mitochondrial Dysfunction', + author: 'Jia D, Tian Z, Wang R', + journal: 'Ageing Research Reviews', + publicationIssue: '2023;91:102087', + doi: '10.1016/j.arr.2023.102087', + }, + { + citationNo: 7, + title: 'Exercise as medicine - evidence for prescribing exercise as therapy in 26 different chronic diseases', + author: 'Pedersen BK, Saltin B', + journal: 'Scand J Med Sci Sports', + publicationIssue: '2015 Dec:25 Suppl 3:1-72', + doi: '10.1111/sms.12581', + }, +]; + +export default exerciseBenefitsReferenceData; From c5485d0e0833de546d181e8510a32ff86c37e6e7 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Mon, 4 Nov 2024 02:10:35 -0800 Subject: [PATCH 11/31] Initial commit of pass1b-06 study assay-tissue visualization component --- src/MainStudy/pass1b06AssayTissueTreeData.js | 162 +++++++++++++++++++ src/MainStudy/studyAssays.jsx | 139 ++++++++++++++++ 2 files changed, 301 insertions(+) create mode 100644 src/MainStudy/pass1b06AssayTissueTreeData.js create mode 100644 src/MainStudy/studyAssays.jsx diff --git a/src/MainStudy/pass1b06AssayTissueTreeData.js b/src/MainStudy/pass1b06AssayTissueTreeData.js new file mode 100644 index 00000000..e20697f6 --- /dev/null +++ b/src/MainStudy/pass1b06AssayTissueTreeData.js @@ -0,0 +1,162 @@ +const pass1b06AssayTissueTreeData = [ + [undefined, 'PASS1B-06'], + ['PASS1B-06', 'Transcriptomics'], + ['PASS1B-06', 'Untargeted Proteomics'], + ['PASS1B-06', 'Untargeted Metabolomics'], + ['PASS1B-06', 'Targeted Metabolomics'], + ['PASS1B-06', 'Epigenomics'], + ['Epigenomics', 'RRBS'], + ['Epigenomics', 'ATAC-seq'], + ['Targeted Metabolomics', 'Targeted Tricarboxylic Acid Cycle'], + ['Targeted Metabolomics', 'Targeted Oxylipins'], + ['Targeted Metabolomics', 'Targeted Nucleotides'], + ['Targeted Metabolomics', 'Targeted Keto Acids'], + ['Targeted Metabolomics', 'Targeted Ethanolamides'], + ['Targeted Metabolomics', 'Targeted Amines'], + ['Targeted Metabolomics', 'Targeted Acyl-CoA'], + ['Untargeted Metabolomics', 'Untargeted Reversed-Phase Positive'], + ['Untargeted Metabolomics', 'Untargeted Reversed-Phase Negative'], + ['Untargeted Metabolomics', 'Untargeted Lipidomics Reversed-Phase Positive'], + ['Untargeted Metabolomics', 'Untargeted Lipidomics Reversed-Phase Negative'], + ['Untargeted Metabolomics', 'Untargeted Ion-Pair Negative'], + ['Untargeted Metabolomics', 'Untargeted HILIC-Positive'], + ['Untargeted Proteomics', 'Protein Ubiquitination'], + ['Untargeted Proteomics', 'Global Proteomics'], + ['Untargeted Proteomics', 'Phosphoproteomics'], + ['Untargeted Proteomics', 'Acetyl Proteomics'], + ['Transcriptomics', 'RNA-seq'], + ['ATAC-seq', 'White Adipose'], + ['ATAC-seq', 'Brown Adipose'], + ['ATAC-seq', 'Liver'], + ['ATAC-seq', 'Lung'], + ['ATAC-seq', 'Kidney'], + ['ATAC-seq', 'Heart'], + ['ATAC-seq', 'Gastrocnemius'], + ['ATAC-seq', 'Hippocampus'], + ['RRBS', 'White Adipose'], + ['RRBS', 'Brown Adipose'], + ['RRBS', 'Liver'], + ['RRBS', 'Lung'], + ['RRBS', 'Kidney'], + ['RRBS', 'Heart'], + ['RRBS', 'Gastrocnemius'], + ['RRBS', 'Hippocampus'], + ['Targeted Tricarboxylic Acid Cycle', 'White Adipose'], + ['Targeted Tricarboxylic Acid Cycle', 'Brown Adipose'], + ['Targeted Tricarboxylic Acid Cycle', 'Liver'], + ['Targeted Tricarboxylic Acid Cycle', 'Lung'], + ['Targeted Tricarboxylic Acid Cycle', 'Kidney'], + ['Targeted Tricarboxylic Acid Cycle', 'Heart'], + ['Targeted Tricarboxylic Acid Cycle', 'Gastrocnemius'], + ['Targeted Tricarboxylic Acid Cycle', 'Hippocampus'], + ['Targeted Oxylipins', 'White Adipose'], + ['Targeted Oxylipins', 'Brown Adipose'], + ['Targeted Oxylipins', 'Liver'], + ['Targeted Oxylipins', 'Lung'], + ['Targeted Oxylipins', 'Kidney'], + ['Targeted Oxylipins', 'Heart'], + ['Targeted Oxylipins', 'Gastrocnemius'], + ['Targeted Oxylipins', 'Hippocampus'], + ['Targeted Nucleotides', 'White Adipose'], + ['Targeted Nucleotides', 'Liver'], + ['Targeted Nucleotides', 'Heart'], + ['Targeted Nucleotides', 'Gastrocnemius'], + ['Targeted Keto Acids', 'White Adipose'], + ['Targeted Keto Acids', 'Liver'], + ['Targeted Keto Acids', 'Heart'], + ['Targeted Keto Acids', 'Gastrocnemius'], + ['Targeted Ethanolamides', 'White Adipose'], + ['Targeted Ethanolamides', 'Brown Adipose'], + ['Targeted Ethanolamides', 'Liver'], + ['Targeted Ethanolamides', 'Lung'], + ['Targeted Ethanolamides', 'Kidney'], + ['Targeted Ethanolamides', 'Heart'], + ['Targeted Ethanolamides', 'Gastrocnemius'], + ['Targeted Ethanolamides', 'Hippocampus'], + ['Targeted Amines', 'White Adipose'], + ['Targeted Amines', 'Brown Adipose'], + ['Targeted Amines', 'Liver'], + ['Targeted Amines', 'Lung'], + ['Targeted Amines', 'Kidney'], + ['Targeted Amines', 'Heart'], + ['Targeted Amines', 'Gastrocnemius'], + ['Targeted Amines', 'Hippocampus'], + ['Targeted Acyl-CoA', 'White Adipose'], + ['Targeted Acyl-CoA', 'Liver'], + ['Targeted Acyl-CoA', 'Heart'], + ['Targeted Acyl-CoA', 'Gastrocnemius'], + ['Untargeted Reversed-Phase Positive', 'White Adipose'], + ['Untargeted Reversed-Phase Positive', 'Brown Adipose'], + ['Untargeted Reversed-Phase Positive', 'Liver'], + ['Untargeted Reversed-Phase Positive', 'Lung'], + ['Untargeted Reversed-Phase Positive', 'Kidney'], + ['Untargeted Reversed-Phase Positive', 'Heart'], + ['Untargeted Reversed-Phase Positive', 'Gastrocnemius'], + ['Untargeted Reversed-Phase Positive', 'Hippocampus'], + ['Untargeted Reversed-Phase Negative', 'White Adipose'], + ['Untargeted Reversed-Phase Negative', 'Brown Adipose'], + ['Untargeted Reversed-Phase Negative', 'Liver'], + ['Untargeted Reversed-Phase Negative', 'Lung'], + ['Untargeted Reversed-Phase Negative', 'Kidney'], + ['Untargeted Reversed-Phase Negative', 'Heart'], + ['Untargeted Reversed-Phase Negative', 'Gastrocnemius'], + ['Untargeted Reversed-Phase Negative', 'Hippocampus'], + ['Untargeted Lipidomics Reversed-Phase Positive', 'White Adipose'], + ['Untargeted Lipidomics Reversed-Phase Positive', 'Brown Adipose'], + ['Untargeted Lipidomics Reversed-Phase Positive', 'Liver'], + ['Untargeted Lipidomics Reversed-Phase Positive', 'Lung'], + ['Untargeted Lipidomics Reversed-Phase Positive', 'Kidney'], + ['Untargeted Lipidomics Reversed-Phase Positive', 'Heart'], + ['Untargeted Lipidomics Reversed-Phase Positive', 'Gastrocnemius'], + ['Untargeted Lipidomics Reversed-Phase Positive', 'Hippocampus'], + ['Untargeted Lipidomics Reversed-Phase Negative', 'White Adipose'], + ['Untargeted Lipidomics Reversed-Phase Negative', 'Brown Adipose'], + ['Untargeted Lipidomics Reversed-Phase Negative', 'Liver'], + ['Untargeted Lipidomics Reversed-Phase Negative', 'Lung'], + ['Untargeted Lipidomics Reversed-Phase Negative', 'Kidney'], + ['Untargeted Lipidomics Reversed-Phase Negative', 'Heart'], + ['Untargeted Lipidomics Reversed-Phase Negative', 'Gastrocnemius'], + ['Untargeted Lipidomics Reversed-Phase Negative', 'Hippocampus'], + ['Untargeted Ion-Pair Negative', 'White Adipose'], + ['Untargeted Ion-Pair Negative', 'Brown Adipose'], + ['Untargeted Ion-Pair Negative', 'Liver'], + ['Untargeted Ion-Pair Negative', 'Lung'], + ['Untargeted Ion-Pair Negative', 'Kidney'], + ['Untargeted Ion-Pair Negative', 'Heart'], + ['Untargeted Ion-Pair Negative', 'Gastrocnemius'], + ['Untargeted Ion-Pair Negative', 'Hippocampus'], + ['Untargeted HILIC-Positive', 'White Adipose'], + ['Untargeted HILIC-Positive', 'Brown Adipose'], + ['Untargeted HILIC-Positive', 'Liver'], + ['Untargeted HILIC-Positive', 'Lung'], + ['Untargeted HILIC-Positive', 'Kidney'], + ['Untargeted HILIC-Positive', 'Heart'], + ['Untargeted HILIC-Positive', 'Gastrocnemius'], + ['Untargeted HILIC-Positive', 'Hippocampus'], + ['Protein Ubiquitination', 'Liver'], + ['Protein Ubiquitination', 'Heart'], + ['Global Proteomics', 'White Adipose'], + ['Global Proteomics', 'Liver'], + ['Global Proteomics', 'Lung'], + ['Global Proteomics', 'Kidney'], + ['Global Proteomics', 'Heart'], + ['Global Proteomics', 'Gastrocnemius'], + ['Phosphoproteomics', 'White Adipose'], + ['Phosphoproteomics', 'Liver'], + ['Phosphoproteomics', 'Lung'], + ['Phosphoproteomics', 'Kidney'], + ['Phosphoproteomics', 'Heart'], + ['Phosphoproteomics', 'Gastrocnemius'], + ['Acetyl Proteomics', 'Liver'], + ['Acetyl Proteomics', 'Heart'], + ['RNA-seq', 'White Adipose'], + ['RNA-seq', 'Brown Adipose'], + ['RNA-seq', 'Liver'], + ['RNA-seq', 'Lung'], + ['RNA-seq', 'Kidney'], + ['RNA-seq', 'Heart'], + ['RNA-seq', 'Gastrocnemius'], + ['RNA-seq', 'Hippocampus'], +]; + +export default pass1b06AssayTissueTreeData; diff --git a/src/MainStudy/studyAssays.jsx b/src/MainStudy/studyAssays.jsx new file mode 100644 index 00000000..0c580e8a --- /dev/null +++ b/src/MainStudy/studyAssays.jsx @@ -0,0 +1,139 @@ +import React from 'react'; +import { Link } from 'react-router-dom'; +import { Helmet } from 'react-helmet'; +import Highcharts from 'highcharts'; +import HighchartsReact from 'highcharts-react-official'; +import PageTitle from '../lib/ui/pageTitle'; +import ExternalLink from '../lib/ui/externalLink'; +import pass1b06AssayTissueTreeData from './pass1b06AssayTissueTreeData'; + +// Import order is important! +require('highcharts/modules/treemap')(Highcharts); +require('highcharts/modules/treegraph')(Highcharts); +require('highcharts/modules/boost')(Highcharts); +require('highcharts/modules/exporting')(Highcharts); +require('highcharts/modules/export-data')(Highcharts); + +function StudyAssays() { + // Highcharts options + const chartOptions = { + chart: { + spacingBottom: 30, + marginRight: 120, + height: 2000, + }, + title: { + align: 'center', + style: { + fontSize: '1.5rem', + }, + text: 'Enduarance trained young adult rats study assays', + }, + tooltip: { + enabled: false, + }, + series: [ + { + type: 'treegraph', + keys: ['parent', 'id', 'level'], + clip: false, + data: pass1b06AssayTissueTreeData, + marker: { + symbol: 'circle', + radius: 6, + fillColor: '#FFFFFF', + lineWidth: 3, + }, + dataLabels: { + align: 'left', + pointFormat: '{point.id}', + style: { + color: '#000000', + textOutline: '3px #ffffff', + whiteSpace: 'nowrap', + }, + x: 16, + crop: false, + overflow: 'none', + }, + levels: [ + { + level: 1, + levelIsConstant: false, + }, + { + level: 2, + colorByPoint: true, + }, + { + level: 3, + colorVariation: { + key: 'brightness', + to: -0.5, + }, + }, + { + level: 4, + colorVariation: { + key: 'brightness', + to: 0.5, + }, + marker: { + radius: 4, + }, + dataLabels: { + x: 10, + }, + }, + ], + }, + ], + credits: { + enabled: false, + }, + legend: { + squareSymbol: true, + symbolWidth: 25, + }, + exporting: { + enabled: true, + }, + }; + + return ( +
    + + + Assays in MoTrPAC Studies - MoTrPAC Data Hub + + +
    +
    +
    +
    +

    Endurance trained young adult rats study

    +
    +
    +

    + Below is a visual guide to the assays performed in the endurance + trained young adult rats study. Click on a node to expand or + collapse it. +

    +
    +
    +
    + +
    +
    +
    +
    +
    +
    + ); +} + +export default StudyAssays; From 0a3ce661fb5fe5669f9dcfa0b2af7a9dd2211094 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Mon, 4 Nov 2024 02:13:44 -0800 Subject: [PATCH 12/31] Add styling for exercise benefits citation list --- src/sass/mainStudy/_mainStudyPage.scss | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/src/sass/mainStudy/_mainStudyPage.scss b/src/sass/mainStudy/_mainStudyPage.scss index 3c4b0b18..35c729ee 100644 --- a/src/sass/mainStudy/_mainStudyPage.scss +++ b/src/sass/mainStudy/_mainStudyPage.scss @@ -71,6 +71,14 @@ } } +.exerciseBenefitsPage { + .exercise-benefits-page-content-container { + .cexercise-benefits-itation-list { + padding-left: 20px; + } + } +} + // disable react-wordcloud tooltip div[data-tippy-root=""] { display: none !important; From a7d54308429b734db6c04877d5305056beec0995 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Mon, 4 Nov 2024 02:20:37 -0800 Subject: [PATCH 13/31] Update unit tests due to route changes --- src/App/__test__/App.test.jsx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/App/__test__/App.test.jsx b/src/App/__test__/App.test.jsx index a72acc89..2007a80a 100644 --- a/src/App/__test__/App.test.jsx +++ b/src/App/__test__/App.test.jsx @@ -23,7 +23,7 @@ describe('', () => { }); test('It should contain fifteen children', () => { - expect(component.find('Route').length).toBe(21); + expect(component.find('Route').length).toBe(23); }); test('It should contain four children', () => { @@ -81,7 +81,7 @@ describe('Unauthenticated Application routing', () => { test('loads the browse data page at /project-overview', () => { history.push('/project-overview'); mountApp.update(); - testCorrectComponentInPath(mountApp, 'Route', 'MainStudy', '/project-overview', history); + testCorrectComponentInPath(mountApp, 'Route', 'ProjectOverview', '/project-overview', history); }); test('loads the linkout page at /external-links', () => { From 0d7e955063c17671092dde21fa12f83d15bfabd2 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 5 Nov 2024 01:06:26 -0800 Subject: [PATCH 14/31] Initial commit of pass1b-06 assay-tissue mapping table component --- src/MainStudy/pass1b06AssayTissueTable.jsx | 144 +++++++++++++++++++++ 1 file changed, 144 insertions(+) create mode 100644 src/MainStudy/pass1b06AssayTissueTable.jsx diff --git a/src/MainStudy/pass1b06AssayTissueTable.jsx b/src/MainStudy/pass1b06AssayTissueTable.jsx new file mode 100644 index 00000000..12127e49 --- /dev/null +++ b/src/MainStudy/pass1b06AssayTissueTable.jsx @@ -0,0 +1,144 @@ +import React from 'react'; +import pass1b06AssayTissueJson from './pass1b_06_assay_tissue.json'; +import pass1b06AssayByOmicJson from './pass1b_06_assay_by_omic.json'; + +const capitalize = (str) => str.replace(/\b\w/g, (char) => char.toUpperCase()); + +function Pass1b06AssayTissueTable() { + return ( +
    + {/* Render epigenomics assay table */} +

    Epigenomics

    +
    + + + + + + + + + {pass1b06AssayByOmicJson['epigenomics'].map((item) => ( + + + + + ))} + +
    AssayTissues
    {item.assay} + {pass1b06AssayTissueJson['epigenomics'][item.id].map((tissue) => ( + + {capitalize(tissue.split('-').slice(1).join('-').replace(/-/g, ' '))} + + ))} +
    +
    + {/* Render metabolomics-targeted assay table */} +

    Targeted Metabolomics

    +
    + + + + + + + + + {pass1b06AssayByOmicJson['metabolomics-targeted'].map((item) => ( + + + + + ))} + +
    AssayTissues
    {item.assay} + {pass1b06AssayTissueJson['metabolomics-targeted'][item.id].map((tissue) => ( + + {capitalize(tissue.split('-').slice(1).join('-').replace(/-/g, ' '))} + + ))} +
    +
    + {/* Render metabolomics-untargeted assay table */} +

    Untargeted Metabolomics

    +
    + + + + + + + + + {pass1b06AssayByOmicJson['metabolomics-untargeted'].map((item) => ( + + + + + ))} + +
    AssayTissues
    {item.assay} + {pass1b06AssayTissueJson['metabolomics-untargeted'][item.id].map((tissue) => ( + + {capitalize(tissue.split('-').slice(1).join('-').replace(/-/g, ' '))} + + ))} +
    +
    + {/* Render proteomics-untargeted assay table */} +

    Untargeted Proteomics

    +
    + + + + + + + + + {pass1b06AssayByOmicJson['proteomics-untargeted'].map((item) => ( + + + + + ))} + +
    AssayTissues
    {item.assay} + {pass1b06AssayTissueJson['proteomics-untargeted'][item.id].map((tissue) => ( + + {capitalize(tissue.split('-').slice(1).join('-').replace(/-/g, ' '))} + + ))} +
    +
    + {/* Render transcriptomics assay table */} +

    Transcriptomics

    +
    + + + + + + + + + {pass1b06AssayByOmicJson['transcriptomics'].map((item) => ( + + + + + ))} + +
    AssayTissues
    {item.assay} + {pass1b06AssayTissueJson['transcriptomics'][item.id].map((tissue) => ( + + {capitalize(tissue.split('-').slice(1).join('-').replace(/-/g, ' '))} + + ))} +
    +
    +
    + ); +} + +export default Pass1b06AssayTissueTable; From 78d0bb999dbc0f5bfa2131f15c87f607e7688824 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 5 Nov 2024 01:07:18 -0800 Subject: [PATCH 15/31] Initial commit of assays by ome JSON data --- src/MainStudy/pass1b_06_assay_by_omic.json | 92 ++++++++++++++++++++++ 1 file changed, 92 insertions(+) create mode 100644 src/MainStudy/pass1b_06_assay_by_omic.json diff --git a/src/MainStudy/pass1b_06_assay_by_omic.json b/src/MainStudy/pass1b_06_assay_by_omic.json new file mode 100644 index 00000000..bb30af82 --- /dev/null +++ b/src/MainStudy/pass1b_06_assay_by_omic.json @@ -0,0 +1,92 @@ +{ + "transcriptomics": [ + { + "id": "transcript-rna-seq", + "assay": "RNA-seq" + } + ], + "epigenomics": [ + { + "id": "epigen-atac-seq", + "assay": "ATAC-seq" + }, + { + "id": "epigen-rrbs", + "assay": "RRBS" + } + ], + "metabolomics-targeted": [ + { + "id": "metab-t-acoa", + "assay": "Targeted Acyl-CoA" + }, + { + "id": "metab-t-amines", + "assay": "Targeted Amines" + }, + { + "id": "metab-t-etamidpos", + "assay": "Targeted Ethanolamides" + }, + { + "id": "metab-t-ka", + "assay": "Targeted Keto Acids" + }, + { + "id": "metab-t-nuc", + "assay": "Targeted Nucleotides" + }, + { + "id": "metab-t-oxylipneg", + "assay": "Targeted Oxylipins" + }, + { + "id": "metab-t-tca", + "assay": "Targeted Tricarboxylic Acid Cycle" + } + ], + "metabolomics-untargeted": [ + { + "id": "metab-u-hilicpos", + "assay": "Untargeted HILIC-Positive" + }, + { + "id": "metab-u-ionpneg", + "assay": "Untargeted Ion-Pair Negative" + }, + { + "id": "metab-u-lrpneg", + "assay": "Untargeted Lipidomics Reversed-Phase Negative" + }, + { + "id": "metab-u-lrppos", + "assay": "Untargeted Lipidomics Reversed-Phase Positive" + }, + { + "id": "metab-u-rpneg", + "assay": "Untargeted Reversed-Phase Negative" + }, + { + "id": "metab-u-rppos", + "assay": "Untargeted Reversed-Phase Positive" + } + ], + "proteomics-untargeted": [ + { + "id": "prot-ac", + "assay": "Acetyl Proteomics" + }, + { + "id": "prot-ph", + "assay": "Phosphoproteomics" + }, + { + "id": "prot-pr", + "assay": "Global Proteomics" + }, + { + "id": "prot-ub", + "assay": "Protein Ubiquitination" + } + ] +} \ No newline at end of file From da118e5abe6698aa938ee479769f77f442e101be Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 5 Nov 2024 01:08:14 -0800 Subject: [PATCH 16/31] Initial commit of incomplete assay-tissue mapping JSON data --- src/MainStudy/pass1b_06_assay_tissue.json | 184 ++++++++++++++++++++++ 1 file changed, 184 insertions(+) create mode 100644 src/MainStudy/pass1b_06_assay_tissue.json diff --git a/src/MainStudy/pass1b_06_assay_tissue.json b/src/MainStudy/pass1b_06_assay_tissue.json new file mode 100644 index 00000000..eb8804c9 --- /dev/null +++ b/src/MainStudy/pass1b_06_assay_tissue.json @@ -0,0 +1,184 @@ +{ + "epigenomics": { + "epigen-atac-seq": [ + "t52-hippocampus", + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t69-brown-adipose", + "t70-white-adipose" + ], + "epigen-rrbs": [ + "t52-hippocampus", + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t69-brown-adipose", + "t70-white-adipose" + ] + }, + "metabolomics-targeted": { + "metab-t-acoa": [ + "t55-gastrocnemius", + "t58-heart", + "t68-liver", + "t70-white-adipose" + ], + "metab-t-amines": [ + "t52-hippocampus", + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t69-brown-adipose", + "t70-white-adipose" + ], + "metab-t-etamidpos": [ + "t52-hippocampus", + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t69-brown-adipose", + "t70-white-adipose" + ], + "metab-t-ka": [ + "t55-gastrocnemius", + "t58-heart", + "t68-liver", + "t70-white-adipose" + ], + "metab-t-nuc": [ + "t55-gastrocnemius", + "t58-heart", + "t68-liver", + "t70-white-adipose" + ], + "metab-t-oxylipneg": [ + "t52-hippocampus", + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t69-brown-adipose", + "t70-white-adipose" + ], + "metab-t-tca": [ + "t52-hippocampus", + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t69-brown-adipose", + "t70-white-adipose" + ] + }, + "metabolomics-untargeted": { + "metab-u-hilicpos": [ + "t52-hippocampus", + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t69-brown-adipose", + "t70-white-adipose" + ], + "metab-u-ionpneg": [ + "t52-hippocampus", + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t69-brown-adipose", + "t70-white-adipose" + ], + "metab-u-lrpneg": [ + "t52-hippocampus", + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t69-brown-adipose", + "t70-white-adipose" + ], + "metab-u-lrppos": [ + "t52-hippocampus", + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t69-brown-adipose", + "t70-white-adipose" + ], + "metab-u-rpneg": [ + "t52-hippocampus", + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t69-brown-adipose", + "t70-white-adipose" + ], + "metab-u-rppos": [ + "t52-hippocampus", + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t69-brown-adipose", + "t70-white-adipose" + ] + }, + "proteomics-untargeted": { + "prot-ac": [ + "t58-heart", + "t68-liver" + ], + "prot-ph": [ + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t70-white-adipose" + ], + "prot-pr": [ + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t70-white-adipose" + ], + "prot-ub": [ + "t58-heart", + "t68-liver" + ] + }, + "transcriptomics": { + "transcript-rna-seq": [ + "t52-hippocampus", + "t55-gastrocnemius", + "t58-heart", + "t59-kidney", + "t66-lung", + "t68-liver", + "t69-brown-adipose", + "t70-white-adipose" + ] + } +} From 4104898ee5321086166c3a6bf94c705ff1cd8702 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 5 Nov 2024 01:09:24 -0800 Subject: [PATCH 17/31] Rename tree graph root node --- src/MainStudy/pass1b06AssayTissueTreeData.js | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/MainStudy/pass1b06AssayTissueTreeData.js b/src/MainStudy/pass1b06AssayTissueTreeData.js index e20697f6..4b03f424 100644 --- a/src/MainStudy/pass1b06AssayTissueTreeData.js +++ b/src/MainStudy/pass1b06AssayTissueTreeData.js @@ -1,10 +1,10 @@ const pass1b06AssayTissueTreeData = [ - [undefined, 'PASS1B-06'], - ['PASS1B-06', 'Transcriptomics'], - ['PASS1B-06', 'Untargeted Proteomics'], - ['PASS1B-06', 'Untargeted Metabolomics'], - ['PASS1B-06', 'Targeted Metabolomics'], - ['PASS1B-06', 'Epigenomics'], + [undefined, 'Rats: Endurance Training'], + ['Rats: Endurance Training', 'Transcriptomics'], + ['Rats: Endurance Training', 'Untargeted Proteomics'], + ['Rats: Endurance Training', 'Untargeted Metabolomics'], + ['Rats: Endurance Training', 'Targeted Metabolomics'], + ['Rats: Endurance Training', 'Epigenomics'], ['Epigenomics', 'RRBS'], ['Epigenomics', 'ATAC-seq'], ['Targeted Metabolomics', 'Targeted Tricarboxylic Acid Cycle'], From 23bc2e8ed668c4d2380e90219a6d6e4ed23fcd0b Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 5 Nov 2024 01:11:16 -0800 Subject: [PATCH 18/31] Updated UI to show either table or graph views of assay-tissue mappings by toggle --- src/MainStudy/studyAssays.jsx | 74 +++++++++++++++++++++++++---------- 1 file changed, 53 insertions(+), 21 deletions(-) diff --git a/src/MainStudy/studyAssays.jsx b/src/MainStudy/studyAssays.jsx index 0c580e8a..37a9465f 100644 --- a/src/MainStudy/studyAssays.jsx +++ b/src/MainStudy/studyAssays.jsx @@ -1,4 +1,4 @@ -import React from 'react'; +import React, { useState } from 'react'; import { Link } from 'react-router-dom'; import { Helmet } from 'react-helmet'; import Highcharts from 'highcharts'; @@ -6,6 +6,7 @@ import HighchartsReact from 'highcharts-react-official'; import PageTitle from '../lib/ui/pageTitle'; import ExternalLink from '../lib/ui/externalLink'; import pass1b06AssayTissueTreeData from './pass1b06AssayTissueTreeData'; +import Pass1b06AssayTissueTable from './pass1b06AssayTissueTable'; // Import order is important! require('highcharts/modules/treemap')(Highcharts); @@ -15,6 +16,7 @@ require('highcharts/modules/exporting')(Highcharts); require('highcharts/modules/export-data')(Highcharts); function StudyAssays() { + const [assayView, setAssayView] = useState('table'); // Highcharts options const chartOptions = { chart: { @@ -27,7 +29,7 @@ function StudyAssays() { style: { fontSize: '1.5rem', }, - text: 'Enduarance trained young adult rats study assays', + text: 'Click on a node to expand or collapse its child nodes', }, tooltip: { enabled: false, @@ -100,35 +102,65 @@ function StudyAssays() { }, }; + function handleViewChange(view) { + setAssayView(view); + } + return ( -
    +
    Assays in MoTrPAC Studies - MoTrPAC Data Hub -
    +
    -
    -
    +
    +

    Endurance trained young adult rats study

    -
    -
    -

    - Below is a visual guide to the assays performed in the endurance - trained young adult rats study. Click on a node to expand or - collapse it. -

    -
    -
    -
    - +
    + +
    + {assayView === 'table' && ( +
    + +
    + )} + {assayView === 'graph' && ( +
    +
    + +
    +
    + )}
    From 445162ba3541f6121a40bdfd5b86041fccf18a2f Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 5 Nov 2024 01:11:53 -0800 Subject: [PATCH 19/31] Add styling for assay-tissue mappings table --- src/sass/mainStudy/_mainStudyPage.scss | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/src/sass/mainStudy/_mainStudyPage.scss b/src/sass/mainStudy/_mainStudyPage.scss index 35c729ee..f3c540fd 100644 --- a/src/sass/mainStudy/_mainStudyPage.scss +++ b/src/sass/mainStudy/_mainStudyPage.scss @@ -79,6 +79,22 @@ } } +.studyAssaysPage { + .study-assays-page-content-container { + .pass1b-06-assay-tissue-table { + table td:first-child { + width: 35%; + } + + .badge-pill { + font-size: 0.8rem; + font-weight: 500; + padding: 0.3rem 0.65rem; + } + } + } +} + // disable react-wordcloud tooltip div[data-tippy-root=""] { display: none !important; From 45b15edb11d130b447aeb6ea2c1eec5ac0c4cef2 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Thu, 7 Nov 2024 16:53:23 -0800 Subject: [PATCH 20/31] Add new route to data license component --- src/App/App.jsx | 2 ++ src/App/__test__/App.test.jsx | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/src/App/App.jsx b/src/App/App.jsx index f32861fe..6c355304 100644 --- a/src/App/App.jsx +++ b/src/App/App.jsx @@ -29,6 +29,7 @@ import ProjectOverviewConnected from '../MainStudy/overview'; import ExerciseBenefits from '../MainStudy/exerciseBenefits'; import StudyAssays from '../MainStudy/studyAssays'; import Tutorials from '../Tutorials/tutorials'; +import License from '../License/licensePage'; import Publications from '../Publications/publications'; import MultiOmicsWorkingGroups from '../MultiOmicsWorkingGroups/multiOmicsWorkingGroups'; import FullTableEnduranceTraining from '../Publications/Data/Animal/Phenotype/fullTableEnduranceTraining'; @@ -147,6 +148,7 @@ function App({ history = History }) { component={withTracker(StudyAssays)} /> + ', () => { }); test('It should contain fifteen children', () => { - expect(component.find('Route').length).toBe(23); + expect(component.find('Route').length).toBe(24); }); test('It should contain four children', () => { From b021b2d33ea7558d2b36bd4e13e7d19c9a0fd291 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Thu, 7 Nov 2024 16:54:54 -0800 Subject: [PATCH 21/31] Add data license clause --- src/BrowseDataPage/components/dataDownloadsMain.jsx | 7 +++++-- src/Search/searchPage.jsx | 11 +++++++++-- 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/src/BrowseDataPage/components/dataDownloadsMain.jsx b/src/BrowseDataPage/components/dataDownloadsMain.jsx index 3fdb2219..66e25563 100644 --- a/src/BrowseDataPage/components/dataDownloadsMain.jsx +++ b/src/BrowseDataPage/components/dataDownloadsMain.jsx @@ -55,8 +55,11 @@ function DataDownloadsMain({

    Explore and download the MoTrPAC multi-omics datasets, which includes quantitative results and analyses of molecular changes from - exercise across tissues. Currently, the complete young rat endurance - training dataset is publicly available. + exercise across tissues. Currently, the complete young adult rat endurance + training dataset is publicly available and provided under the + {' '} + CC BY 4.0 license + . {' '} {userType && userType === 'internal' ? 'The young rat acute exercise and human precovid sedentary adult datasets are currently available to consortium members only in the early preview phase. ' diff --git a/src/Search/searchPage.jsx b/src/Search/searchPage.jsx index 3e02c94b..f0242aad 100644 --- a/src/Search/searchPage.jsx +++ b/src/Search/searchPage.jsx @@ -169,14 +169,21 @@ export function SearchPage({

    - Search by gene ID, protein ID or metabolite name to examine the + Search by gene symbol, protein ID or metabolite name to examine the timewise endurance training response over 8 weeks of training in - adult rats.{' '} + young adult rats. + {' '} Multiple search terms MUST be separated by comma and space. Examples: "NP_001000006.1, NP_001001508.2, NP_001005898.3" or "8,9-EpETrE, C18:1 LPC plasmalogen B". + {' '} + The endurance trained young adult rats dataset is made available + under the + {' '} + CC BY 4.0 license + .
    From ca76516973050a248d95972c48a4c3d6f65cf924 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Thu, 7 Nov 2024 16:55:36 -0800 Subject: [PATCH 22/31] Add software and data license clauses --- src/CodeRepoPage/codeRepoPage.jsx | 20 ++++++++++++++++++-- 1 file changed, 18 insertions(+), 2 deletions(-) diff --git a/src/CodeRepoPage/codeRepoPage.jsx b/src/CodeRepoPage/codeRepoPage.jsx index 84da7b47..bc149e52 100644 --- a/src/CodeRepoPage/codeRepoPage.jsx +++ b/src/CodeRepoPage/codeRepoPage.jsx @@ -1,7 +1,9 @@ import React from 'react'; +import { Link } from 'react-router-dom'; import { Helmet } from 'react-helmet'; import PageTitle from '../lib/ui/pageTitle'; import IconSet from '../lib/iconSet'; +import ExternalLink from '../lib/ui/externalLink'; const repositories = { pipelines: [ @@ -102,10 +104,24 @@ export function CodeRepositories() {
    -
    +

    Explore the source codes integral to the workflow of the MoTrPAC data, from ingestion to analysis. -

    +

    +

    + The MoTrPAC open source repositories are hosted on GitHub and + provided under the + {' '} + + . The data available through the MoTrPAC Data Hub portal is + provided under the + {' '} + CC BY 4.0 license + . +

    {renderRepoComponent('Pipelines', repositories.pipelines)} From f17c92c400ac15f3fd62a2987e90e69eba7dbd52 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Thu, 7 Nov 2024 16:56:45 -0800 Subject: [PATCH 23/31] Initial commit of data license component --- src/License/licensePage.jsx | 40 +++++++++++++++++++++++++++++++++++++ src/sass/_license.scss | 10 ++++++++++ src/sass/main.scss | 1 + 3 files changed, 51 insertions(+) create mode 100644 src/License/licensePage.jsx create mode 100644 src/sass/_license.scss diff --git a/src/License/licensePage.jsx b/src/License/licensePage.jsx new file mode 100644 index 00000000..e746e0a2 --- /dev/null +++ b/src/License/licensePage.jsx @@ -0,0 +1,40 @@ +import React from 'react'; +import { Helmet } from 'react-helmet'; +import PageTitle from '../lib/ui/pageTitle'; +import ExternalLink from '../lib/ui/externalLink'; + +function License() { + return ( +
    + + + MoTrPAC Data License - MoTrPAC Data Hub + + +
    +
    +

    + The data available through the MoTrPAC Data Hub portal is provided + under the Creative Commons Attribution 4.0 International License + (CC BY 4.0). This license allows users to use, share, adapt, distribute, + and reproduce the data in any medium or format, provided appropriate + credit is given to the original author(s) and the source, a link to the + Creative Commons license is included, and any modifications are clearly + indicated. +

    +

    + To view the full terms of this license, please visit Creative Commons + Attribution 4.0 International License (CC BY 4.0) at + {' '} + +

    +
    +
    +
    + ); +} + +export default License; diff --git a/src/sass/_license.scss b/src/sass/_license.scss new file mode 100644 index 00000000..4e268fd1 --- /dev/null +++ b/src/sass/_license.scss @@ -0,0 +1,10 @@ +.licensePage { + margin-bottom: 1.25rem; + + .license-content-container { + .material-icons { + font-size: 1.25rem; + line-height: 1.65; + } + } +} diff --git a/src/sass/main.scss b/src/sass/main.scss index 6d7be81c..88ff68fd 100644 --- a/src/sass/main.scss +++ b/src/sass/main.scss @@ -39,3 +39,4 @@ @import 'publications'; @import 'multiOmicsWorkingGroups'; @import 'reactLiteYoutubeEmbed'; +@import 'license'; From 8f302436c3acd8b0f8e1fed9e5b7a16ed7a48321 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Thu, 7 Nov 2024 16:57:19 -0800 Subject: [PATCH 24/31] Add dropdown menu link to data license --- src/Navbar/navbar.jsx | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/Navbar/navbar.jsx b/src/Navbar/navbar.jsx index 2435fdde..d46ffe23 100644 --- a/src/Navbar/navbar.jsx +++ b/src/Navbar/navbar.jsx @@ -363,6 +363,9 @@ export function Navbar({ Tutorials + + License +
  • From 9c4a8d01d8af110129af31d1ee564b126e26776a Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Thu, 7 Nov 2024 16:58:25 -0800 Subject: [PATCH 25/31] Add styling for external link icon to MIT license --- src/sass/codeRepo/_codeRepo.scss | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/sass/codeRepo/_codeRepo.scss b/src/sass/codeRepo/_codeRepo.scss index 42e75716..0735888b 100644 --- a/src/sass/codeRepo/_codeRepo.scss +++ b/src/sass/codeRepo/_codeRepo.scss @@ -1,7 +1,12 @@ .codeRepoPage { .code-repo-content-container { .code-repo-summary-container { - margin-bottom: 2.5em; + margin-bottom: 2.0em; + + .material-icons { + font-size: 1.25rem; + line-height: 1.65; + } } .code-repo-container { From acc16a5f430919ac5e7d23072d3500b4fc3279a8 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Thu, 7 Nov 2024 17:00:35 -0800 Subject: [PATCH 26/31] Add styling to PASS1B-06 study title on assay-tissue mapping page --- src/MainStudy/studyAssays.jsx | 5 ++++- src/sass/mainStudy/_mainStudyPage.scss | 14 ++++++++++++++ 2 files changed, 18 insertions(+), 1 deletion(-) diff --git a/src/MainStudy/studyAssays.jsx b/src/MainStudy/studyAssays.jsx index 37a9465f..78075ff8 100644 --- a/src/MainStudy/studyAssays.jsx +++ b/src/MainStudy/studyAssays.jsx @@ -117,7 +117,10 @@ function StudyAssays() {
    -

    Endurance trained young adult rats study

    +

    + pest_control_rodent + Endurance trained young adult rats study +

    + {/* Metabolomics data deposition table */} +

    Metabolomics (Targeted and Untargeted)

    +
    + + + + + + + + + + + + + + + +
    RepositoryData typeProject
    + + Metabolomics raw + results files (identification and quantification) +
      +
    • + +
      • +
    • + +
      • +
    +
    +
    + {/* Proteomics data deposition table */} +

    Proteomics

    +
    + + + + + + + + + + + + + diff --git a/src/sass/_dataDeposition.scss b/src/sass/_dataDeposition.scss new file mode 100644 index 00000000..15dfaec9 --- /dev/null +++ b/src/sass/_dataDeposition.scss @@ -0,0 +1,21 @@ +.dataDepositionPage { + .data-deposition-content-container { + table { + td:first-child { + width: 23%; + } + + td:last-child { + width: 22%; + } + + ul { + margin-bottom: 0; + + &.proteomics-data-submissions { + padding-left: 15px; + } + } + } + } +} \ No newline at end of file diff --git a/src/sass/main.scss b/src/sass/main.scss index 88ff68fd..1c7680b5 100644 --- a/src/sass/main.scss +++ b/src/sass/main.scss @@ -40,3 +40,4 @@ @import 'multiOmicsWorkingGroups'; @import 'reactLiteYoutubeEmbed'; @import 'license'; +@import 'dataDeposition'; From 99c707e24bd5c3817f735569d3d5cf76d18394e2 Mon Sep 17 00:00:00 2001 From: Jimmy Zhen Date: Tue, 12 Nov 2024 22:28:04 -0800 Subject: [PATCH 31/31] Update PASS1B-06 assay-to-tissue mappings --- src/MainStudy/pass1b06AssayTissueTreeData.js | 34 ++++++++++++++++++ src/MainStudy/pass1b_06_assay_tissue.json | 38 ++++++++++++++++++-- src/MainStudy/studyAssays.jsx | 2 +- 3 files changed, 71 insertions(+), 3 deletions(-) diff --git a/src/MainStudy/pass1b06AssayTissueTreeData.js b/src/MainStudy/pass1b06AssayTissueTreeData.js index 4b03f424..438496cf 100644 --- a/src/MainStudy/pass1b06AssayTissueTreeData.js +++ b/src/MainStudy/pass1b06AssayTissueTreeData.js @@ -49,6 +49,7 @@ const pass1b06AssayTissueTreeData = [ ['Targeted Tricarboxylic Acid Cycle', 'Heart'], ['Targeted Tricarboxylic Acid Cycle', 'Gastrocnemius'], ['Targeted Tricarboxylic Acid Cycle', 'Hippocampus'], + ['Targeted Tricarboxylic Acid Cycle', 'Plasma'], ['Targeted Oxylipins', 'White Adipose'], ['Targeted Oxylipins', 'Brown Adipose'], ['Targeted Oxylipins', 'Liver'], @@ -57,6 +58,7 @@ const pass1b06AssayTissueTreeData = [ ['Targeted Oxylipins', 'Heart'], ['Targeted Oxylipins', 'Gastrocnemius'], ['Targeted Oxylipins', 'Hippocampus'], + ['Targeted Oxylipins', 'Plasma'], ['Targeted Nucleotides', 'White Adipose'], ['Targeted Nucleotides', 'Liver'], ['Targeted Nucleotides', 'Heart'], @@ -65,6 +67,7 @@ const pass1b06AssayTissueTreeData = [ ['Targeted Keto Acids', 'Liver'], ['Targeted Keto Acids', 'Heart'], ['Targeted Keto Acids', 'Gastrocnemius'], + ['Targeted Keto Acids', 'Plasma'], ['Targeted Ethanolamides', 'White Adipose'], ['Targeted Ethanolamides', 'Brown Adipose'], ['Targeted Ethanolamides', 'Liver'], @@ -73,6 +76,7 @@ const pass1b06AssayTissueTreeData = [ ['Targeted Ethanolamides', 'Heart'], ['Targeted Ethanolamides', 'Gastrocnemius'], ['Targeted Ethanolamides', 'Hippocampus'], + ['Targeted Ethanolamides', 'Plasma'], ['Targeted Amines', 'White Adipose'], ['Targeted Amines', 'Brown Adipose'], ['Targeted Amines', 'Liver'], @@ -81,6 +85,7 @@ const pass1b06AssayTissueTreeData = [ ['Targeted Amines', 'Heart'], ['Targeted Amines', 'Gastrocnemius'], ['Targeted Amines', 'Hippocampus'], + ['Targeted Amines', 'Plasma'], ['Targeted Acyl-CoA', 'White Adipose'], ['Targeted Acyl-CoA', 'Liver'], ['Targeted Acyl-CoA', 'Heart'], @@ -93,6 +98,7 @@ const pass1b06AssayTissueTreeData = [ ['Untargeted Reversed-Phase Positive', 'Heart'], ['Untargeted Reversed-Phase Positive', 'Gastrocnemius'], ['Untargeted Reversed-Phase Positive', 'Hippocampus'], + ['Untargeted Reversed-Phase Positive', 'Plasma'], ['Untargeted Reversed-Phase Negative', 'White Adipose'], ['Untargeted Reversed-Phase Negative', 'Brown Adipose'], ['Untargeted Reversed-Phase Negative', 'Liver'], @@ -101,6 +107,7 @@ const pass1b06AssayTissueTreeData = [ ['Untargeted Reversed-Phase Negative', 'Heart'], ['Untargeted Reversed-Phase Negative', 'Gastrocnemius'], ['Untargeted Reversed-Phase Negative', 'Hippocampus'], + ['Untargeted Reversed-Phase Negative', 'Plasma'], ['Untargeted Lipidomics Reversed-Phase Positive', 'White Adipose'], ['Untargeted Lipidomics Reversed-Phase Positive', 'Brown Adipose'], ['Untargeted Lipidomics Reversed-Phase Positive', 'Liver'], @@ -109,6 +116,7 @@ const pass1b06AssayTissueTreeData = [ ['Untargeted Lipidomics Reversed-Phase Positive', 'Heart'], ['Untargeted Lipidomics Reversed-Phase Positive', 'Gastrocnemius'], ['Untargeted Lipidomics Reversed-Phase Positive', 'Hippocampus'], + ['Untargeted Lipidomics Reversed-Phase Positive', 'Plasma'], ['Untargeted Lipidomics Reversed-Phase Negative', 'White Adipose'], ['Untargeted Lipidomics Reversed-Phase Negative', 'Brown Adipose'], ['Untargeted Lipidomics Reversed-Phase Negative', 'Liver'], @@ -117,6 +125,7 @@ const pass1b06AssayTissueTreeData = [ ['Untargeted Lipidomics Reversed-Phase Negative', 'Heart'], ['Untargeted Lipidomics Reversed-Phase Negative', 'Gastrocnemius'], ['Untargeted Lipidomics Reversed-Phase Negative', 'Hippocampus'], + ['Untargeted Lipidomics Reversed-Phase Negative', 'Plasma'], ['Untargeted Ion-Pair Negative', 'White Adipose'], ['Untargeted Ion-Pair Negative', 'Brown Adipose'], ['Untargeted Ion-Pair Negative', 'Liver'], @@ -125,14 +134,26 @@ const pass1b06AssayTissueTreeData = [ ['Untargeted Ion-Pair Negative', 'Heart'], ['Untargeted Ion-Pair Negative', 'Gastrocnemius'], ['Untargeted Ion-Pair Negative', 'Hippocampus'], + ['Untargeted Ion-Pair Negative', 'Plasma'], + ['Untargeted HILIC-Positive', 'Vena Cava'], ['Untargeted HILIC-Positive', 'White Adipose'], ['Untargeted HILIC-Positive', 'Brown Adipose'], ['Untargeted HILIC-Positive', 'Liver'], + ['Untargeted HILIC-Positive', 'Small Intestine'], ['Untargeted HILIC-Positive', 'Lung'], + ['Untargeted HILIC-Positive', 'Ovaries'], + ['Untargeted HILIC-Positive', 'Testes'], + ['Untargeted HILIC-Positive', 'Spleen'], + ['Untargeted HILIC-Positive', 'Colon'], + ['Untargeted HILIC-Positive', 'Adrenal'], ['Untargeted HILIC-Positive', 'Kidney'], ['Untargeted HILIC-Positive', 'Heart'], + ['Untargeted HILIC-Positive', 'Vastus Lateralis'], ['Untargeted HILIC-Positive', 'Gastrocnemius'], + ['Untargeted HILIC-Positive', 'Hypothalamus'], + ['Untargeted HILIC-Positive', 'Cortex'], ['Untargeted HILIC-Positive', 'Hippocampus'], + ['Untargeted HILIC-Positive', 'Plasma'], ['Protein Ubiquitination', 'Liver'], ['Protein Ubiquitination', 'Heart'], ['Global Proteomics', 'White Adipose'], @@ -141,22 +162,35 @@ const pass1b06AssayTissueTreeData = [ ['Global Proteomics', 'Kidney'], ['Global Proteomics', 'Heart'], ['Global Proteomics', 'Gastrocnemius'], + ['Global Proteomics', 'Cortex'], ['Phosphoproteomics', 'White Adipose'], ['Phosphoproteomics', 'Liver'], ['Phosphoproteomics', 'Lung'], ['Phosphoproteomics', 'Kidney'], ['Phosphoproteomics', 'Heart'], ['Phosphoproteomics', 'Gastrocnemius'], + ['Phosphoproteomics', 'Cortex'], ['Acetyl Proteomics', 'Liver'], ['Acetyl Proteomics', 'Heart'], + ['RNA-seq', 'Vena Cava'], ['RNA-seq', 'White Adipose'], ['RNA-seq', 'Brown Adipose'], ['RNA-seq', 'Liver'], + ['RNA-seq', 'Small Intestine'], ['RNA-seq', 'Lung'], + ['RNA-seq', 'Ovaries'], + ['RNA-seq', 'Testes'], + ['RNA-seq', 'Spleen'], + ['RNA-seq', 'Colon'], + ['RNA-seq', 'Adrenal'], ['RNA-seq', 'Kidney'], ['RNA-seq', 'Heart'], + ['RNA-seq', 'Vastus Lateralis'], ['RNA-seq', 'Gastrocnemius'], + ['RNA-seq', 'Hypothalamus'], + ['RNA-seq', 'Cortex'], ['RNA-seq', 'Hippocampus'], + ['RNA-seq', 'Blood Rna'], ]; export default pass1b06AssayTissueTreeData; diff --git a/src/MainStudy/pass1b_06_assay_tissue.json b/src/MainStudy/pass1b_06_assay_tissue.json index eb8804c9..1bde6e57 100644 --- a/src/MainStudy/pass1b_06_assay_tissue.json +++ b/src/MainStudy/pass1b_06_assay_tissue.json @@ -29,6 +29,7 @@ "t70-white-adipose" ], "metab-t-amines": [ + "t31-plasma", "t52-hippocampus", "t55-gastrocnemius", "t58-heart", @@ -39,6 +40,7 @@ "t70-white-adipose" ], "metab-t-etamidpos": [ + "t31-plasma", "t52-hippocampus", "t55-gastrocnemius", "t58-heart", @@ -49,6 +51,7 @@ "t70-white-adipose" ], "metab-t-ka": [ + "t31-plasma", "t55-gastrocnemius", "t58-heart", "t68-liver", @@ -61,6 +64,7 @@ "t70-white-adipose" ], "metab-t-oxylipneg": [ + "t31-plasma", "t52-hippocampus", "t55-gastrocnemius", "t58-heart", @@ -71,6 +75,7 @@ "t70-white-adipose" ], "metab-t-tca": [ + "t31-plasma", "t52-hippocampus", "t55-gastrocnemius", "t58-heart", @@ -83,16 +88,28 @@ }, "metabolomics-untargeted": { "metab-u-hilicpos": [ + "t31-plasma", "t52-hippocampus", + "t53-cortex", + "t54-hypothalamus", "t55-gastrocnemius", + "t56-vastus-lateralis", "t58-heart", "t59-kidney", + "t60-adrenal", + "t61-colon", + "t62-spleen", + "t63-testes", + "t64-ovaries", "t66-lung", + "t67-small-intestine", "t68-liver", "t69-brown-adipose", - "t70-white-adipose" + "t70-white-adipose", + "t99-vena-cava" ], "metab-u-ionpneg": [ + "t31-plasma", "t52-hippocampus", "t55-gastrocnemius", "t58-heart", @@ -103,6 +120,7 @@ "t70-white-adipose" ], "metab-u-lrpneg": [ + "t31-plasma", "t52-hippocampus", "t55-gastrocnemius", "t58-heart", @@ -113,6 +131,7 @@ "t70-white-adipose" ], "metab-u-lrppos": [ + "t31-plasma", "t52-hippocampus", "t55-gastrocnemius", "t58-heart", @@ -123,6 +142,7 @@ "t70-white-adipose" ], "metab-u-rpneg": [ + "t31-plasma", "t52-hippocampus", "t55-gastrocnemius", "t58-heart", @@ -133,6 +153,7 @@ "t70-white-adipose" ], "metab-u-rppos": [ + "t31-plasma", "t52-hippocampus", "t55-gastrocnemius", "t58-heart", @@ -149,6 +170,7 @@ "t68-liver" ], "prot-ph": [ + "t53-cortex", "t55-gastrocnemius", "t58-heart", "t59-kidney", @@ -157,6 +179,7 @@ "t70-white-adipose" ], "prot-pr": [ + "t53-cortex", "t55-gastrocnemius", "t58-heart", "t59-kidney", @@ -171,14 +194,25 @@ }, "transcriptomics": { "transcript-rna-seq": [ + "t30-blood-rna", "t52-hippocampus", + "t53-cortex", + "t54-hypothalamus", "t55-gastrocnemius", + "t56-vastus-lateralis", "t58-heart", "t59-kidney", + "t60-adrenal", + "t61-colon", + "t62-spleen", + "t63-testes", + "t64-ovaries", "t66-lung", + "t67-small-intestine", "t68-liver", "t69-brown-adipose", - "t70-white-adipose" + "t70-white-adipose", + "t99-vena-cava" ] } } diff --git a/src/MainStudy/studyAssays.jsx b/src/MainStudy/studyAssays.jsx index 78075ff8..9c738539 100644 --- a/src/MainStudy/studyAssays.jsx +++ b/src/MainStudy/studyAssays.jsx @@ -22,7 +22,7 @@ function StudyAssays() { chart: { spacingBottom: 30, marginRight: 120, - height: 2000, + height: 2600, }, title: { align: 'center',
    RepositoryData typeMetadata
    + + +
      +
    • + + Global Protein Abundance in Gastrocnemius, White Adipose, Cortex, + Lung, and Kidney + + (Dataset ID: MSV000092911) +
      • +
    • + + Protein Phosphorylation in Gastrocnemius, White Adipose Tissue, + Cortex, Lung, and Kidney + + (Dataset ID: MSV000092925) +
      • +
    • + + Global Protein Abundance in Heart and Liver + + (Dataset ID: MSV000092922) +
      • +
    • + + Protein Acetylation in Heart and Liver + + (Dataset ID: MSV000092924) +
      • +
    • + + Protein Phosphorylation in Heart and Liver + + (Dataset ID: MSV000092923) +
      • +
    • + + Protein Ubiquitination in Heart and Liver + + (Dataset ID: MSV000092931) +
      • +
    +     		+
      +
    • + +
      • +
    • + +
      • +