Skip to content

Commit

Permalink
Squashed commit of the following:
Browse files Browse the repository at this point in the history 
commit 8a5116b
Author: ivokwee <[email protected]>
Date:   Tue Mar 21 09:44:26 2023 +0100

    fix code/layout

commit 2fb90f8
Author: ivokwee <[email protected]>
Date:   Tue Mar 21 02:18:31 2023 +0100

    correct modal plot content widths (in progress)

commit 0927cac
Merge: 19f1f38 efea20d
Author: Ivo Kwee <[email protected]>
Date:   Mon Mar 20 23:55:22 2023 +0100

    Merge pull request #251 from bigomics/revert-250-dev-grid-cards

    Revert "Dev-cards-bs5"

commit efea20d
Author: Ivo Kwee <[email protected]>
Date:   Mon Mar 20 23:54:16 2023 +0100

    Revert "Dev-cards-bs5"

commit 19f1f38
Merge: 9a384be 19e445d
Author: Ivo Kwee <[email protected]>
Date:   Mon Mar 20 22:53:20 2023 +0100

    Merge pull request #250 from bigomics/dev-grid-cards

    Dev-cards-bs5. Merging but let's remove for the moment the wireframe  (card outline) and get the original UI look as close as possible.

commit 9a384be
Author: ivokwee <[email protected]>
Date:   Mon Mar 20 20:17:11 2023 +0100

    add pgx in all req() to prevent runtime errors

commit 826ffd7
Merge: f838b45 8fb6509
Author: ivokwee <[email protected]>
Date:   Mon Mar 20 20:15:25 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit f838b45
Author: ivokwee <[email protected]>
Date:   Mon Mar 20 20:15:20 2023 +0100

    correct drug-tab tabrequire

commit 8fb6509
Author: ncullen93 <[email protected]>
Date:   Mon Mar 20 17:04:56 2023 +0000

    fix: account for cluster rank in group labels

commit 5c9529b
Author: ivokwee <[email protected]>
Date:   Mon Mar 20 16:02:50 2023 +0100

    correct function.name

commit ff7ab08
Author: ivokwee <[email protected]>
Date:   Mon Mar 20 16:01:06 2023 +0100

    version rc3

commit e8b86f4
Author: ivokwee <[email protected]>
Date:   Mon Mar 20 16:00:17 2023 +0100

    remove dbg

commit a2fbe0b
Author: ivokwee <[email protected]>
Date:   Mon Mar 20 15:59:26 2023 +0100

    correct shiny detection

commit 19e445d
Author: Mauro Masiero <[email protected]>
Date:   Mon Mar 20 15:56:12 2023 +0100

    source `cards.scss`

commit 16872c5
Author: Mauro Masiero <[email protected]>
Date:   Mon Mar 20 15:56:00 2023 +0100

    feat: remove info button from plot

commit 4bd9f41
Author: Mauro Masiero <[email protected]>
Date:   Mon Mar 20 15:55:27 2023 +0100

    feat: reduce card padding

commit e00fa9e
Author: Mauro Masiero <[email protected]>
Date:   Mon Mar 20 15:41:54 2023 +0100

    remove class plotmodule

commit 98a759e
Author: Mauro Masiero <[email protected]>
Date:   Mon Mar 20 15:37:46 2023 +0100

    add footer background color

commit 4504d69
Author: Mauro Masiero <[email protected]>
Date:   Mon Mar 20 15:37:32 2023 +0100

    remove browser

commit 2e2ac9c
Merge: 50c2997 78e668a
Author: Mauro Masiero <[email protected]>
Date:   Mon Mar 20 15:11:20 2023 +0100

    Merge branch 'dev-grid-cards' of https://github.com/bigomics/omicsplayground into dev-grid-cards

commit 78e668a
Author: Xavier Escribà Montagut <[email protected]>
Date:   Mon Mar 20 15:08:45 2023 +0100

    fix: placed cards inside div + removed full screen

    somehow, this allows the updateInputs to work, not sure why otherwise they are not working

commit 50c2997
Author: Mauro Masiero <[email protected]>
Date:   Mon Mar 20 15:03:27 2023 +0100

    feat: add footer to cards

commit 75fae68
Author: Mauro Masiero <[email protected]>
Date:   Mon Mar 20 14:08:56 2023 +0100

    feat: cards implemented in plot module

commit e11fd30
Merge: 4b468f7 6124138
Author: ivokwee <[email protected]>
Date:   Mon Mar 20 10:36:56 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit 4b468f7
Author: ivokwee <[email protected]>
Date:   Mon Mar 20 10:36:52 2023 +0100

    restore default OPTIONS

commit 6124138
Author: Mauro Masiero <[email protected]>
Date:   Mon Mar 20 07:55:13 2023 +0100

    improve distance between welcome page buttons

commit 8b60ed2
Author: ivokwee <[email protected]>
Date:   Mon Mar 20 01:34:51 2023 +0100

    update

commit cd76e0f
Author: ivokwee <[email protected]>
Date:   Mon Mar 20 01:30:20 2023 +0100

    rename to declared->defined

commit 0aa240a
Author: ivokwee <[email protected]>
Date:   Mon Mar 20 01:10:44 2023 +0100

    add code analyzer

commit fc8a0dd
Author: ivokwee <[email protected]>
Date:   Sun Mar 19 21:33:22 2023 +0100

    resolve issue #238 with caption overlap: decrease scrollY in table

commit fe29fa4
Author: ivokwee <[email protected]>
Date:   Sun Mar 19 20:15:26 2023 +0100

    revert to prev welcom message

commit 6696212
Merge: 0bbaeb5 a21f003
Author: Ivo Kwee <[email protected]>
Date:   Sun Mar 19 20:11:57 2023 +0100

    Merge pull request #247 from bigomics/dev-home

    Dev home

commit a21f003
Merge: aa093c4 0bbaeb5
Author: Ivo Kwee <[email protected]>
Date:   Sun Mar 19 20:11:38 2023 +0100

    Merge branch 'master' into dev-home

commit 0bbaeb5
Author: ivokwee <[email protected]>
Date:   Sun Mar 19 20:04:43 2023 +0100

    cleanup & cosmetics

commit aa093c4
Author: Mauro Masiero <[email protected]>
Date:   Sun Mar 19 18:32:33 2023 +0100

    feat: allow user to load example-data multiple times

commit 9802741
Author: Mauro Masiero <[email protected]>
Date:   Sun Mar 19 18:12:47 2023 +0100

    feat: center align modal dialog pop up; remove css that gets overwritten by bs5

commit a4063a6
Author: ivokwee <[email protected]>
Date:   Sun Mar 19 06:35:24 2023 +0100

    edit CSS layout tables & sft

commit 9cda1d4
Author: ivokwee <[email protected]>
Date:   Sun Mar 19 03:06:45 2023 +0100

    small refactor

commit d4e77d0
Author: ivokwee <[email protected]>
Date:   Sun Mar 19 02:16:51 2023 +0100

    add copyright header

commit cade4f9
Author: ivokwee <[email protected]>
Date:   Sun Mar 19 02:01:20 2023 +0100

    edit credits

commit b2172b8
Author: ivokwee <[email protected]>
Date:   Sun Mar 19 01:57:18 2023 +0100

    edit credits

commit 5ec1a1e
Author: ivokwee <[email protected]>
Date:   Sun Mar 19 01:54:22 2023 +0100

    edit credits

commit 8ea8122
Author: ivokwee <[email protected]>
Date:   Sun Mar 19 01:35:47 2023 +0100

    update creditse && git push

commit c09d4b3
Author: ivokwee <[email protected]>
Date:   Sun Mar 19 01:32:12 2023 +0100

    add credit popup

commit 1473c70
Author: ivokwee <[email protected]>
Date:   Sat Mar 18 23:59:41 2023 +0100

    add file

commit 94a09e2
Author: ivokwee <[email protected]>
Date:   Sat Mar 18 23:59:02 2023 +0100

    lots of little changes

commit b32defd
Author: Mauro Masiero <[email protected]>
Date:   Sat Mar 18 20:00:58 2023 +0100

    improve existing user text

commit 9961936
Author: Mauro Masiero <[email protected]>
Date:   Sat Mar 18 18:54:10 2023 +0100

    improving load example data description for user

commit 180ca73
Author: Mauro Masiero <[email protected]>
Date:   Sat Mar 18 18:47:18 2023 +0100

    add cursor pointer on logo mouse hover

commit fefeb8d
Author: Mauro Masiero <[email protected]>
Date:   Sat Mar 18 18:25:23 2023 +0100

    welcome board now triggered

commit 9ced0a8
Author: Mauro Masiero <[email protected]>
Date:   Sat Mar 18 18:13:25 2023 +0100

    click on logo trigger successful

commit 03f2256
Author: Mauro Masiero <[email protected]>
Date:   Sat Mar 18 17:51:18 2023 +0100

    add id to logo bigomics

commit 892d284
Author: Mauro Masiero <[email protected]>
Date:   Sat Mar 18 17:50:03 2023 +0100

    removing code that is overwriting correct styles

commit 7080f00
Author: Mauro Masiero <[email protected]>
Date:   Sat Mar 18 17:37:42 2023 +0100

    improving modal dialog box size in all screens screens

commit 90848bb
Author: ivokwee <[email protected]>
Date:   Sat Mar 18 01:46:12 2023 +0100

    correct zoom plot layout

commit be35a75
Author: ivokwee <[email protected]>
Date:   Fri Mar 17 23:51:09 2023 +0100

    labels bit up

commit e38a6ff
Merge: 835698c 6bde44a
Author: ivokwee <[email protected]>
Date:   Fri Mar 17 23:11:38 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit 835698c
Author: ivokwee <[email protected]>
Date:   Fri Mar 17 23:11:34 2023 +0100

    add ensable/disable upload

commit 6bde44a
Author: Xavier Escribà Montagut <[email protected]>
Date:   Fri Mar 17 17:18:00 2023 +0100

    feat: plotly defaults added globally

commit fe00711
Author: Xavier Escribà Montagut <[email protected]>
Date:   Fri Mar 17 17:14:51 2023 +0100

    feat: plot editor embedded

commit d1d1110
Author: ivokwee <[email protected]>
Date:   Fri Mar 17 14:57:47 2023 +0100

    remove xtitle

commit 574024f
Author: ivokwee <[email protected]>
Date:   Fri Mar 17 14:29:59 2023 +0100

    correct layout

commit 2afdcfb
Author: ivokwee <[email protected]>
Date:   Fri Mar 17 13:53:11 2023 +0100

    fix csv output format digits

commit 33909ff
Author: ivokwee <[email protected]>
Date:   Fri Mar 17 13:28:14 2023 +0100

    move install RSpectra to base image

commit f2f43aa
Author: ivokwee <[email protected]>
Date:   Fri Mar 17 13:27:24 2023 +0100

    fix layout KEGG tab

commit ce7b533
Author: ivokwee <[email protected]>
Date:   Fri Mar 17 12:58:09 2023 +0100

    align tabs

commit 92d8aac
Author: ivokwee <[email protected]>
Date:   Fri Mar 17 01:26:03 2023 +0100

    update scss

commit 6cba0b1
Author: ivokwee <[email protected]>
Date:   Fri Mar 17 01:25:20 2023 +0100

    update scss

commit 5800dc5
Author: ivokwee <[email protected]>
Date:   Fri Mar 17 00:21:33 2023 +0100

    version rc1

commit fed2027
Author: ivokwee <[email protected]>
Date:   Fri Mar 17 00:04:04 2023 +0100

    show version at start

commit 4f02fa8
Author: ivokwee <[email protected]>
Date:   Thu Mar 16 23:53:13 2023 +0100

    fix layout and clean up code

commit 08ac085
Author: ncullen93 <[email protected]>
Date:   Thu Mar 16 16:53:02 2023 +0100

    add icons to table menu and left-align text

commit e4e1419
Merge: ef7da8f 619d0ac
Author: ncullen93 <[email protected]>
Date:   Thu Mar 16 11:41:16 2023 -0400

    Merge pull request #241 from bigomics/share-datasets

    Share datasets

commit 619d0ac
Merge: 655efc7 ef7da8f
Author: ncullen93 <[email protected]>
Date:   Thu Mar 16 11:41:07 2023 -0400

    Merge branch 'master' into share-datasets

commit ef7da8f
Author: ivokwee <[email protected]>
Date:   Thu Mar 16 16:39:01 2023 +0100

    enable hide/show of main menu items (issue #224)

commit c8d5933
Author: ivokwee <[email protected]>
Date:   Thu Mar 16 16:36:00 2023 +0100

    add refs

commit 661fe2a
Author: ivokwee <[email protected]>
Date:   Thu Mar 16 16:35:16 2023 +0100

    add beta labels in menu

commit 13cafbf
Merge: 2a7e8ee bd2fa9e
Author: Ivo Kwee <[email protected]>
Date:   Thu Mar 16 16:28:41 2023 +0100

    Merge pull request #240 from bigomics/loading-tsne

    make separate shared tsne

commit 655efc7
Author: ncullen93 <[email protected]>
Date:   Thu Mar 16 15:36:40 2023 +0100

    download zip now works

commit dadabfc
Author: ncullen93 <[email protected]>
Date:   Thu Mar 16 15:25:14 2023 +0100

    all buttons besides zip work

commit 2a7e8ee
Author: ivokwee <[email protected]>
Date:   Thu Mar 16 13:38:04 2023 +0100

    make caption 13px

commit bd2fa9e
Author: ivokwee <[email protected]>
Date:   Thu Mar 16 13:33:06 2023 +0100

    make separate shared tsne

commit e832b77
Author: ivokwee <[email protected]>
Date:   Thu Mar 16 12:11:51 2023 +0100

    rename tab names

commit e7e24ed
Merge: 489774b 44e1c57
Author: ivokwee <[email protected]>
Date:   Thu Mar 16 12:10:55 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit 489774b
Author: ivokwee <[email protected]>
Date:   Thu Mar 16 12:10:42 2023 +0100

    add loading dbg output

commit 8475a56
Author: ncullen93 <[email protected]>
Date:   Thu Mar 16 11:36:36 2023 +0100

    add action menus to table

commit 44e1c57
Merge: 23c280c 03128f6
Author: Mauro Masiero <[email protected]>
Date:   Thu Mar 16 11:28:58 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit 23c280c
Author: Mauro Masiero <[email protected]>
Date:   Thu Mar 16 11:28:55 2023 +0100

    plot_table_geneset_map now plotly

commit 00c282d
Author: Mauro Masiero <[email protected]>
Date:   Thu Mar 16 11:28:39 2023 +0100

    plot_table_gene_map now plotly

commit 03128f6
Merge: 642780f ef1f7b1
Author: ivokwee <[email protected]>
Date:   Thu Mar 16 10:56:40 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit 642780f
Author: ivokwee <[email protected]>
Date:   Thu Mar 16 10:56:36 2023 +0100

    add grid breakpoint xxxl=2400px & using single bootstrap row

commit ef1f7b1
Author: Mauro Masiero <[email protected]>
Date:   Thu Mar 16 10:21:05 2023 +0100

    solve issue #237

commit 73f4d73
Author: Mauro Masiero <[email protected]>
Date:   Wed Mar 15 22:37:09 2023 +0100

    remove browser

commit aaf667b
Author: Mauro Masiero <[email protected]>
Date:   Wed Mar 15 17:55:18 2023 +0100

    move FILES to reactive function

commit d305589
Author: Mauro Masiero <[email protected]>
Date:   Wed Mar 15 17:09:25 2023 +0100

    fix selector on kegg_table_server

commit d49e92a
Author: ivokwee <[email protected]>
Date:   Wed Mar 15 16:35:29 2023 +0100

    change layout

commit 83f23ab
Author: ivokwee <[email protected]>
Date:   Wed Mar 15 15:33:49 2023 +0100

    add Specra r package

commit 2e2d092
Author: ncullen93 <[email protected]>
Date:   Wed Mar 15 15:28:01 2023 +0100

    confirmation dialog added to share dataset

commit 284624a
Author: ncullen93 <[email protected]>
Date:   Wed Mar 15 14:21:23 2023 +0100

    user datasets can now be shared; missing modal confirmation before sharing though

commit b0d465e
Author: ncullen93 <[email protected]>
Date:   Wed Mar 15 11:52:03 2023 +0100

    welcomeboard: close right sidebar when going to load data page

commit e7c8f28
Author: ncullen93 <[email protected]>
Date:   Wed Mar 15 11:16:12 2023 +0100

    board.loading: buttons in shared dataset table also now disabled when no dataset selected

commit a3b2bef
Author: ncullen93 <[email protected]>
Date:   Wed Mar 15 10:46:14 2023 +0100

    board.loading: buttons are disabled when no dataset is selected

commit 24d399e
Author: ncullen93 <[email protected]>
Date:   Wed Mar 15 10:11:00 2023 +0100

    remove hover feature on board.loading buttons

commit 9483cea
Author: ncullen93 <[email protected]>
Date:   Wed Mar 15 09:58:57 2023 +0100

    make table color of selected row a bit darker

commit cdd1c34
Author: ncullen93 <[email protected]>
Date:   Wed Mar 15 09:45:12 2023 +0100

    board.loading: tsne plot now aligns with datasets table

commit 59f9062
Author: Xavier Escribà Montagut <[email protected]>
Date:   Tue Mar 14 23:08:27 2023 +0100

    feat: embed plotly editor on iframe modal

commit 8ddb9b3
Author: mauromiguelm <[email protected]>
Date:   Tue Mar 14 17:32:08 2023 +0100

    fix: tsneplot width bug

commit 881ee5c
Merge: fd44cd3 1e19913
Author: Mauro Masiero <[email protected]>
Date:   Tue Mar 14 17:23:14 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit fd44cd3
Author: Mauro Masiero <[email protected]>
Date:   Tue Mar 14 17:23:11 2023 +0100

    update requirements

commit 1e19913
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 15:48:37 2023 +0100

    fix: pgxtable displays correctly after loading example dataset

commit 698ee35
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 13:44:52 2023 +0100

    remove all remaining inputData refs

commit 080820a
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 13:43:25 2023 +0100

    boards compare + tcga + wgcna: ngs + inputData -> pgx

commit 07db192
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 13:37:45 2023 +0100

    board.singlecell: ngs + inputData -> pgx

commit e7848da
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 13:33:49 2023 +0100

    board.connectivity: ngs + inputData -> pgx

commit 15ded9c
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 13:30:58 2023 +0100

    board.biomarker: ngs + inputData -> pgx

commit 4cec562
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 13:29:24 2023 +0100

    board.correlation: ngs + inputData -> pgx

commit ae8a32b
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 13:26:59 2023 +0100

    board.signature: ngs + inputData -> pgx

commit fb7cd2b
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 13:24:31 2023 +0100

    board.intersection: ngs + inputData -> pgx

commit ff18b5e
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 11:50:03 2023 +0100

    board.drugconnectivity: inputData + ngs -> pgx

commit 1b0850c
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 11:45:51 2023 +0100

    board.functional: inputData + ngs -> pgx

commit 10906ce
Merge: 7dd9127 051035b
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 06:41:36 2023 -0400

    Merge pull request #227 from bigomics/FeatureMapBoard-to-pgx

    remove inputData and ngs refs in favor of pgx

commit 7dd9127
Merge: 4801d3b f582e31
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 06:41:25 2023 -0400

    Merge pull request #228 from bigomics/EnrichmentBoard-to-pgx

    replace ngs and inputData with pgx

commit f582e31
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 11:40:46 2023 +0100

    replace ngs and inputData with pgx

commit 051035b
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 11:33:34 2023 +0100

    remove inputData and ngs refs in favor of pgx

commit 4801d3b
Merge: b86405d 2831095
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 11:24:27 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit b86405d
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 11:24:19 2023 +0100

    better validate message for gene table

commit 2831095
Merge: b1e1ec1 724e40c
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 06:17:26 2023 -0400

    Merge pull request #226 from bigomics/fix-diffexpr-blinking

    fix: diffexpr plots blink and initialize to all genes selected

commit 724e40c
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 11:16:21 2023 +0100

    fix: diffexpr plots blink and initialize to all genes selected

commit b1e1ec1
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 10:51:46 2023 +0100

    fix: pgxtable blank after uploading dataset

commit 057ac22
Merge: b40633a fdea6cf
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 04:59:36 2023 -0400

    Merge pull request #221 from bigomics/js-to-shiny

    create Shiny wrappers around bigdash JS triggers... end of JS PITA..

commit fdea6cf
Merge: b9abcc6 b40633a
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 04:59:29 2023 -0400

    Merge branch 'master' into js-to-shiny

commit b40633a
Merge: 6fd984a 0e0e71b
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 04:57:57 2023 -0400

    Merge pull request #223 from bigomics/inputData-pgx-convert

    Input data pgx convert

commit 0e0e71b
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 09:56:53 2023 +0100

    expression board to pgx

commit 176cb41
Author: ncullen93 <[email protected]>
Date:   Tue Mar 14 09:49:38 2023 +0100

    board.expression converted to pgx

commit 6fd984a
Author: ivokwee <[email protected]>
Date:   Tue Mar 14 04:11:51 2023 +0100

    reverting temporary

commit 7656054
Author: ivokwee <[email protected]>
Date:   Tue Mar 14 04:07:24 2023 +0100

    stupid mistake

commit b9abcc6
Author: ivokwee <[email protected]>
Date:   Tue Mar 14 03:41:59 2023 +0100

    create Shiny wrappers around bigdash JS triggers... end of JS PITA..

commit 6a7acec
Author: ivokwee <[email protected]>
Date:   Tue Mar 14 00:28:42 2023 +0100

    move paddings settings to bigdash css

commit 3191420
Merge: 4d63fcf c91ae0e
Author: ivokwee <[email protected]>
Date:   Tue Mar 14 00:27:25 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit 4d63fcf
Author: ivokwee <[email protected]>
Date:   Tue Mar 14 00:27:20 2023 +0100

    add bigdash.selectTab

commit c91ae0e
Author: mauromiguelm <[email protected]>
Date:   Mon Mar 13 23:22:55 2023 +0100

    passed reload pgx reactives to r_global

    trigger observers in load module from upload module, may have cross reactivity

commit 7a5c316
Merge: c111c3d 0d26550
Author: ivokwee <[email protected]>
Date:   Mon Mar 13 20:09:12 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit c111c3d
Author: ivokwee <[email protected]>
Date:   Mon Mar 13 20:09:07 2023 +0100

    remove message

commit 0d26550
Author: mauromiguelm <[email protected]>
Date:   Mon Mar 13 18:58:53 2023 +0100

    magic line that makes all work

commit 63aef5d
Author: mauromiguelm <[email protected]>
Date:   Mon Mar 13 18:52:58 2023 +0100

    show tabs when data is uploaded

commit 0aab78c
Author: mauromiguelm <[email protected]>
Date:   Mon Mar 13 18:52:30 2023 +0100

    upload works again (!)

commit 7ec31b1
Merge: 7319607 573ace7
Author: ivokwee <[email protected]>
Date:   Mon Mar 13 10:04:01 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit 7319607
Author: ivokwee <[email protected]>
Date:   Mon Mar 13 10:03:56 2023 +0100

    correct mouse detection

commit 573ace7
Author: ncullen93 <[email protected]>
Date:   Mon Mar 13 09:51:54 2023 +0100

    fix issue: clicking load example dataset ran but the page didnt change

commit 54d9377
Author: ivokwee <[email protected]>
Date:   Mon Mar 13 02:58:03 2023 +0100

    add require(magrittr)

commit e6f6e86
Author: ivokwee <[email protected]>
Date:   Mon Mar 13 02:14:40 2023 +0100

    move to boardHeader.R to base

commit 33a60aa
Author: ivokwee <[email protected]>
Date:   Mon Mar 13 01:27:54 2023 +0100

    put KEGGgraph/pathview in base

commit 55cce82
Author: ivokwee <[email protected]>
Date:   Mon Mar 13 00:04:18 2023 +0100

    renaming files

commit 2d2a93d
Author: ivokwee <[email protected]>
Date:   Sun Mar 12 23:52:37 2023 +0100

    move to base/R

commit 8a766bc
Author: ivokwee <[email protected]>
Date:   Sun Mar 12 22:46:21 2023 +0100

    correct name typo DropdownMenu

commit 8825b6b
Merge: e2ddbb0 beedbae
Author: ivokwee <[email protected]>
Date:   Sun Mar 12 20:09:08 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit e2ddbb0
Author: ivokwee <[email protected]>
Date:   Sun Mar 12 20:09:03 2023 +0100

    add KEGGgraph in requirements

commit beedbae
Author: Xavier Escribà Montagut <[email protected]>
Date:   Sun Mar 12 20:04:58 2023 +0100

    fix: missing package

    Package needed for `plotly_json` (plot editor)

commit 8dacc1d
Author: ivokwee <[email protected]>
Date:   Sun Mar 12 18:48:07 2023 +0100

    restore dynamic menu

commit a2f94c6
Author: ivokwee <[email protected]>
Date:   Sun Mar 12 18:47:01 2023 +0100

    correct mem.proc for non-linux

commit 9f6fdb0
Author: mauromiguelm <[email protected]>
Date:   Sun Mar 12 13:53:51 2023 +0100

    fix: reduce pop up size and center elements #198

commit ebfbce6
Author: ivokwee <[email protected]>
Date:   Sun Mar 12 06:49:24 2023 +0100

    restore line height in table

commit 94c890b
Author: ivokwee <[email protected]>
Date:   Sun Mar 12 05:08:26 2023 +0100

    disable renv inside docker

commit 24f3cd8
Merge: b825f7f 7a767a3
Author: ivokwee <[email protected]>
Date:   Sun Mar 12 04:54:52 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit b825f7f
Author: ivokwee <[email protected]>
Date:   Sun Mar 12 04:54:47 2023 +0100

    rm/add extdata packages

commit 7a767a3
Author: ncullen93 <[email protected]>
Date:   Sat Mar 11 12:16:24 2023 +0100

    fixed dataview plot blinking

commit 683f204
Author: ivokwee <[email protected]>
Date:   Sat Mar 11 06:55:02 2023 +0100

    rework menu

commit a46451e
Author: ivokwee <[email protected]>
Date:   Sat Mar 11 02:45:55 2023 +0100

    re-added example data

commit 75bfede
Merge: a3a275c dbfce43
Author: Ivo Kwee <[email protected]>
Date:   Sat Mar 11 02:40:04 2023 +0100

    Merge pull request #205 from bigomics/public-datasets-loading

    Public datasets loading

commit dbfce43
Merge: b865b4b a3a275c
Author: Ivo Kwee <[email protected]>
Date:   Sat Mar 11 02:38:14 2023 +0100

    Merge branch 'master' into public-datasets-loading

commit b865b4b
Author: ivokwee <[email protected]>
Date:   Sat Mar 11 02:34:56 2023 +0100

    renamed public to shared which is more general name for now

commit 5f6aa2b
Author: ivokwee <[email protected]>
Date:   Sat Mar 11 02:03:02 2023 +0100

    pgx_public_dir does not need to be reactive as it should not change like pgx_dir does for different users

commit 1723f0f
Author: ivokwee <[email protected]>
Date:   Sat Mar 11 01:47:41 2023 +0100

    Please refrain from pushing entire reactive lists as arguments; be specific

commit c3ea145
Author: ivokwee <[email protected]>
Date:   Sat Mar 11 01:37:33 2023 +0100

    data_public folder should not be in userdir but always below OPG root

commit a3a275c
Merge: ac50180 db75e85
Author: ivokwee <[email protected]>
Date:   Fri Mar 10 23:29:12 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit ac50180
Author: ivokwee <[email protected]>
Date:   Fri Mar 10 23:29:08 2023 +0100

    add redirection to run.log

commit db75e85
Merge: dfbbb5e cfa6c65
Author: Mauro Masiero <[email protected]>
Date:   Thu Mar 9 21:12:13 2023 +0100

    Merge pull request #204 from bigomics/dev-settings-container

    Dev settings container

commit cfa6c65
Author: mauromiguelm <[email protected]>
Date:   Thu Mar 9 19:23:55 2023 +0100

    add new styles.min.css

commit d36b1f3
Author: mauromiguelm <[email protected]>
Date:   Thu Mar 9 19:23:41 2023 +0100

    add trigger to update state of settings bar

commit dfbbb5e
Author: ivokwee <[email protected]>
Date:   Thu Mar 9 19:05:34 2023 +0100

    correct wordcloud

commit cd19193
Author: ivokwee <[email protected]>
Date:   Thu Mar 9 19:01:43 2023 +0100

    change default

commit 0ad44ed
Merge: f85609a 29470fb
Author: ivokwee <[email protected]>
Date:   Thu Mar 9 18:57:07 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit f85609a
Author: ivokwee <[email protected]>
Date:   Thu Mar 9 18:56:56 2023 +0100

    enable/disable modules and menu

commit 54275c5
Author: ncullen93 <[email protected]>
Date:   Thu Mar 9 18:31:50 2023 +0100

    add second public dataset

commit 6919519
Author: ncullen93 <[email protected]>
Date:   Thu Mar 9 17:18:17 2023 +0100

    import public dataset button works now

commit e0a7b07
Author: ncullen93 <[email protected]>
Date:   Thu Mar 9 13:57:55 2023 +0100

    data public table works

commit fee41e3
Author: ncullen93 <[email protected]>
Date:   Thu Mar 9 10:57:48 2023 +0100

    source changes

commit c852450
Merge: 3060ae1 29470fb
Author: ncullen93 <[email protected]>
Date:   Thu Mar 9 04:33:24 2023 -0500

    Merge branch 'master' into dev-settings-container

commit 734fbef
Author: ncullen93 <[email protected]>
Date:   Wed Mar 8 22:38:24 2023 +0100

    add some example public datasets; create new file for eventual public datasets table module

commit 3060ae1
Author: mauromiguelm <[email protected]>
Date:   Wed Mar 8 17:10:14 2023 +0100

    remove default open settings sidebar at loading dataset page

commit 29470fb
Author: Xavier Escribà Montagut <[email protected]>
Date:   Wed Mar 8 17:08:46 2023 +0100

    fix: little fella disappears properly

commit 9890fd3
Author: mauromiguelm <[email protected]>
Date:   Wed Mar 8 16:18:36 2023 +0100

    remove pointer-event since its preventing mouse listener propagation

commit fe4429b
Author: ncullen93 <[email protected]>
Date:   Wed Mar 8 14:38:16 2023 +0100

    add table

commit 47524b8
Merge: f6a43bf 50d725a
Author: ncullen93 <[email protected]>
Date:   Wed Mar 8 07:43:38 2023 -0500

    Merge pull request #203 from bigomics/edit-data-description

    Edit data description

commit 50d725a
Author: ncullen93 <[email protected]>
Date:   Wed Mar 8 10:52:19 2023 +0100

    make only description column editable

commit 1e335ac
Author: ncullen93 <[email protected]>
Date:   Wed Mar 8 09:39:22 2023 +0100

    actual pgx object is edited

commit f6a43bf
Author: ivokwee <[email protected]>
Date:   Wed Mar 8 01:14:32 2023 +0100

    correct reactive pgx.dir path

commit 81eab0c
Author: ivokwee <[email protected]>
Date:   Wed Mar 8 01:13:35 2023 +0100

    shorten caption in zoom

commit 714f465
Merge: 4c30450 0c47731
Author: ivokwee <[email protected]>
Date:   Wed Mar 8 00:48:36 2023 +0100

    Merge branch 'master' of https://github.com/bigomics/omicsplayground

commit 4c30450
Author: ivokwee <[email protected]>
Date:   Wed Mar 8 00:48:31 2023 +0100

    add mem used in dbg

commit 70ae8d6
Author: ncullen93 <[email protected]>
Date:   Tue Mar 7 16:06:34 2023 +0100

    small table changes

commit 1cbb5d4
Author: ncullen93 <[email protected]>
Date:   Tue Mar 7 10:18:42 2023 +0100

    add note about needing to rewrite actual pgx file

commit af945b5
Author: ncullen93 <[email protected]>
Date:   Tue Mar 7 09:55:21 2023 +0100

    dataset meta info changes get saved to datasets-info.csv

commit 206b8a0
Author: ncullen93 <[email protected]>
Date:   Mon Mar 6 15:22:12 2023 +0100

    edit datatable on loading page

commit 943fb16
Author: mauromiguelm <[email protected]>
Date:   Mon Mar 6 08:14:54 2023 +0100

    loading board now shows settings sidebar by default

commit 8d83fcf
Author: mauromiguelm <[email protected]>
Date:   Thu Mar 2 15:39:06 2023 +0100

    dev-`settings-container`
  • Loading branch information
@ESCRI11
ESCRI11 committed Mar 21, 2023
1 parent 1e1d4d4 commit da98222
Show file tree
Hide file tree
Showing 198 changed files with 11,661 additions and 9,695 deletions.
1 change: 1 addition & 0 deletions .gitignore
View file
Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@ ehthumbs.db
Icon?
Thumbs.db


data/*.pgx
!data/example-data.pgx
data/*.csv
Expand Down
30 changes: 18 additions & 12 deletions Makefile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,27 +29,33 @@ clean.force:
show.branch:
@echo $(BRANCH)

run.docker:
docker.run:
@echo running docker $(TAG) at port 4000
docker run --rm -p 4000:3838 bigomics/omicsplayground:$(TAG)
docker run --rm -it -p 4000:3838 bigomics/omicsplayground:$(TAG)

run.docker2:
docker.run2:
@echo running docker $(TAG) at port 4001
docker run --rm -p 4001:3838 bigomics/omicsplayground:$(TAG)
docker run --rm -it -p 4001:3838 bigomics/omicsplayground:$(TAG)

build.base:
@echo building docker BASE
docker build --no-cache \
-f docker/Dockerfile.base \
-t bigomics/omicsplayground:base-ub2204 .

build.docker:
docker: FORCE
@echo building docker $(TAG)
docker build --no-cache --build-arg TAG=$(TAG) \
-f docker/Dockerfile \
-t bigomics/omicsplayground:$(TAG) .

bash.docker:
docker.base: FORCE
@echo building docker BASE
docker build \
-f docker/Dockerfile.base \
-t bigomics/omicsplayground-base:ub2204 .

docker.test: FORCE
@echo building test docker
docker build --no-cache \
-f docker/Dockerfile.test \
-t bigomics/omicsplayground:test .

docker.bash:
@echo bash into docker $(TAG)
docker run -it -p 3838:3838 bigomics/omicsplayground:$(TAG) /bin/bash

Expand Down
3 changes: 2 additions & 1 deletion VERSION
View file
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
v3.beta.1
v3.0-rc3

- V3.0 release candidate 1 (16 mar 2023)
- First beta release (1 mar 2023)
28 changes: 14 additions & 14 deletions components/00SourceAll.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@ if(!file.exists('00SourceAll.R')) {
source('app/R/modules/AuthenticationModule.R',encoding='UTF-8')
source('app/R/modules/BatchCorrectModule.R',encoding='UTF-8')
source('app/R/modules/ComputePgxModule.R',encoding='UTF-8')
source('app/R/modules/examplePlotModule.R',encoding='UTF-8')
source('app/R/modules/InfoModals.R',encoding='UTF-8')
source('app/R/modules/MakeContrastModule.R',encoding='UTF-8')
source('app/R/modules/NormalizeCountsModule.R',encoding='UTF-8')
Expand All @@ -17,15 +16,11 @@ if(!file.exists('00SourceAll.R')) {
source('app/R/modules/SocialMediaModule.R',encoding='UTF-8')
source('app/R/modules/TimerModule.R',encoding='UTF-8')
source('app/R/modules/WelcomeBoard.R',encoding='UTF-8')
source('app/R/utils/boardHeader.R',encoding='UTF-8')
source('app/R/utils/modalUI.R',encoding='UTF-8')
source('app/R/utils/tooltip.R',encoding='UTF-8')
source('app/R/utils/utils.R',encoding='UTF-8')
source('base/R/auth.R',encoding='UTF-8')
source('base/R/compute2-extra.R',encoding='UTF-8')
source('base/R/compute2-genes.R',encoding='UTF-8')
source('base/R/compute2-genesets.R',encoding='UTF-8')
source('base/R/ggplot-colors.R',encoding='UTF-8')
source('base/R/ggplot-theme.R',encoding='UTF-8')
source('base/R/gset-fisher.r',encoding='UTF-8')
source('base/R/gset-gsea.r',encoding='UTF-8')
Expand Down Expand Up @@ -70,10 +65,17 @@ if(!file.exists('00SourceAll.R')) {
source('base/R/pgx-ui.R',encoding='UTF-8')
source('base/R/pgx-vizpanels.R',encoding='UTF-8')
source('base/R/pgx-wordcloud.R',encoding='UTF-8')
source('base/R/PlotModule.R',encoding='UTF-8')
source('base/R/TableModule.R',encoding='UTF-8')
source('base/R/TableModule2.R',encoding='UTF-8')
source('base/R/ui-bigdashplus.R',encoding='UTF-8')
source('base/R/ui-boardHeader.R',encoding='UTF-8')
source('base/R/ui-code.R',encoding='UTF-8')
source('base/R/ui-colors.R',encoding='UTF-8')
source('base/R/ui-defaults.R',encoding='UTF-8')
source('base/R/ui-DropDownMenu.R',encoding='UTF-8')
source('base/R/ui-modalUI.R',encoding='UTF-8')
source('base/R/ui-PlotModule.R',encoding='UTF-8')
source('base/R/ui-TableModule.R',encoding='UTF-8')
source('base/R/ui-TableModule2.R',encoding='UTF-8')
source('base/R/ui-tooltip.R',encoding='UTF-8')
source('base/R/xcr-graph.r',encoding='UTF-8')
source('base/R/xcr-math.r',encoding='UTF-8')
source('board.biomarker/R/biomarker_plot_boxplots.R',encoding='UTF-8')
Expand Down Expand Up @@ -103,27 +105,25 @@ if(!file.exists('00SourceAll.R')) {
source('board.compare/R/compare_server.R',encoding='UTF-8')
source('board.compare/R/compare_table_corr_score.R',encoding='UTF-8')
source('board.compare/R/compare_ui.R',encoding='UTF-8')
source('board.connectivity/R/connectivity_plot_cmap_FCFCplots.R',encoding='UTF-8')
source('board.connectivity/R/connectivity_plot_cmapPairsPlot.R',encoding='UTF-8')
source('board.connectivity/R/connectivity_plot_connectivityHeatmap.R',encoding='UTF-8')
source('board.connectivity/R/connectivity_plot_connectivityMap.R',encoding='UTF-8')
source('board.connectivity/R/connectivity_plot_cumEnrichmentPlot.R',encoding='UTF-8')
source('board.connectivity/R/connectivity_plot_cumFCplot.R',encoding='UTF-8')
source('board.connectivity/R/connectivity_plot_enrichmentGraph.R',encoding='UTF-8')
source('board.connectivity/R/connectivity_plot_FCFCplots.R',encoding='UTF-8')
source('board.connectivity/R/connectivity_plot_leadingEdgeGraph.R',encoding='UTF-8')
source('board.connectivity/R/connectivity_plot_scatterPlot.R',encoding='UTF-8')
source('board.connectivity/R/connectivity_server.R',encoding='UTF-8')
source('board.connectivity/R/connectivity_table_similarity_scores.R',encoding='UTF-8')
source('board.connectivity/R/connectivity_table_similarity_scores2.R',encoding='UTF-8')
source('board.connectivity/R/connectivity_ui.R',encoding='UTF-8')
source('board.correlation/R/correlation_plot_cor_graph.R',encoding='UTF-8')
source('board.correlation/R/correlation_plot_partial_correlation.R',encoding='UTF-8')
source('board.correlation/R/correlation_plot_correlation_UMAP.R',encoding='UTF-8')
source('board.correlation/R/correlation_plot_scattercorr.R',encoding='UTF-8')
source('board.correlation/R/correlation_plot_table_corr.R',encoding='UTF-8')
source('board.correlation/R/correlation_server.R',encoding='UTF-8')
source('board.correlation/R/correlation_ui.R',encoding='UTF-8')
source('board.dataview/R/dataview_module_geneinfo.R',encoding='UTF-8')
source('board.dataview/R/dataview_plot_abundance.R',encoding='UTF-8')
source('board.dataview/R/dataview_plot_averagecounts.R',encoding='UTF-8')
source('board.dataview/R/dataview_plot_averagerank.R',encoding='UTF-8')
source('board.dataview/R/dataview_plot_boxplot.R',encoding='UTF-8')
source('board.dataview/R/dataview_plot_correlation.R',encoding='UTF-8')
Expand All @@ -141,7 +141,6 @@ if(!file.exists('00SourceAll.R')) {
source('board.dataview/R/dataview_table_resources.R',encoding='UTF-8')
source('board.dataview/R/dataview_table_samples.R',encoding='UTF-8')
source('board.dataview/R/dataview_ui.R',encoding='UTF-8')
source('board.dataview/R/utils.R',encoding='UTF-8')
source('board.drugconnectivity/R/drugconnectivity_plot_actmap.R',encoding='UTF-8')
source('board.drugconnectivity/R/drugconnectivity_plot_cmap_dsea.R',encoding='UTF-8')
source('board.drugconnectivity/R/drugconnectivity_plot_cmap_enplot.R',encoding='UTF-8')
Expand Down Expand Up @@ -200,6 +199,7 @@ if(!file.exists('00SourceAll.R')) {
source('board.intersection/R/intersection_server.R',encoding='UTF-8')
source('board.intersection/R/intersection_ui.R',encoding='UTF-8')
source('board.loading/R/loading_server.R',encoding='UTF-8')
source('board.loading/R/loading_table_datasets_shared.R',encoding='UTF-8')
source('board.loading/R/loading_table_datasets.R',encoding='UTF-8')
source('board.loading/R/loading_tsneplot.R',encoding='UTF-8')
source('board.loading/R/loading_ui.R',encoding='UTF-8')
Expand Down
16 changes: 7 additions & 9 deletions components/app/R/OPTIONS
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,21 +2,19 @@ TITLE = 'Omics Playground'
#AUTHENTICATION = firebase
AUTHENTICATION = none
#AUTHENTICATION = password
ENABLE_USERDIR = FALSE
ENABLE_USERDIR = TRUE
ENABLE_UPLOAD = TRUE
ENABLE_SAVE = TRUE
ENABLE_DELETE = TRUE
MAX_DATASETS = 1000
MAX_DATASETS = 100
MAX_SAMPLES = 2000
MAX_COMPARISONS = 100
MAX_COMPARISONS = 20
MAX_GENES = 20000
MAX_GENESETS = 5000
WATERMARK = TRUE
TIMEOUT = 0
#TIMEOUT = 2400
TIMEOUT = 0
#TIMEOUT = 2400
HONCHO_URL = http://localhost:8000
PLOTLY_EDITOR = https://shiny-plotly-editor.cpsievert.me

#BOARDS_ENABLED = load,view,clust,expr,enrich,isect,func,word,drug,sig,scell,cor,bio,cmap,tcga
#BOARDS_DISABLED = expr,enrich,isect,func,word,drug,sig,scell,cor,bio,cmap,wgcna,tcga,clust,ftmap,comp
#BOARDS_ENABLED = load,view
#BOARDS_ENABLED = welcome,load,upload,view,clustersamples,clusterfeatures,wgcna,diffexpr,corr,enrich,pathway,wordcloud,drug,isect,sig,bio,cmap,comp,tcga,cell
#BOARDS_ENABLED = load,dataview
24 changes: 10 additions & 14 deletions components/app/R/global.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -88,11 +88,11 @@ message(">>>>> LOADING INITIAL LIBS")
library(shiny)
library(shinyBS)
library(grid)
library(ggplot2)
library(concaveman)
#library(ggplot2)
#library(concaveman)
source(file.path(APPDIR,"utils/utils.R"), local = TRUE)
source(file.path(APPDIR,"utils/modalUI.R"), local = TRUE)
source(file.path(APPDIR,"utils/tooltip.R"), local = TRUE)
#source(file.path(APPDIR,"utils/modalUI.R"), local = TRUE)
#source(file.path(APPDIR,"utils/tooltip.R"), local = TRUE)

message("***********************************************")
message("***** RUNTIME ENVIRONMENT VARIABLES ***********")
Expand Down Expand Up @@ -183,15 +183,12 @@ message("*********** READ MODULES/BOARDS ****************")
message("************************************************")


BOARDS <- c("load","view","clust","expr","enrich","isect","func",
"word","drug","sig","scell","cor","bio","cmap","ftmap",
"wgcna", "tcga","multi","system","qa","corsa","comp","user")
BOARDS <- c("welcome","load","upload","dataview","clustersamples","clusterfeatures",
"diffexpr","enrich","isect","pathway","wordcloud","drug","sig","cell","corr","bio","cmap",
"wgcna", "tcga","comp","user")
if(is.null(opt$BOARDS_ENABLED)) opt$BOARDS_ENABLED = BOARDS
if(is.null(opt$BOARDS_DISABLED)) opt$BOARDS_DISABLED = NA

ENABLED <- array(BOARDS %in% opt$BOARDS_ENABLED, dimnames=list(BOARDS))
DISABLED <- array(BOARDS %in% opt$BOARDS_DISABLED, dimnames=list(BOARDS))
ENABLED <- ENABLED & !DISABLED
ENABLED <- array(rep(TRUE,length(BOARDS)),dimnames=list(BOARDS))
ENABLED <- array(BOARDS %in% opt$BOARDS_ENABLED, dimnames=list(BOARDS))

## disable connectivity map if we have no signature database folder
has.sigdb <- length(dir(SIGDB.DIR,pattern="sigdb.*h5"))>0
Expand All @@ -201,7 +198,6 @@ if(has.sigdb==FALSE) ENABLED["cmap"] <- FALSE
MAINTABS = c("DataView","Clustering","Expression","Enrichment",
"Signature","CellProfiling","DEV")


## --------------------------------------------------------------------
## --------------------- HANDLER MANAGER ------------------------------
## --------------------------------------------------------------------
Expand Down Expand Up @@ -281,6 +277,6 @@ message("\n\n")
## Calculate init time
main.init_time <- round(Sys.time() - main.start_time,digits=4)
main.init_time
message("[INIT] main init time = ",main.init_time," ",attr(main.init_time,"units"))
message("[global.R] global init time = ",main.init_time," ",attr(main.init_time,"units"))

shiny::addResourcePath("static", "www")
4 changes: 2 additions & 2 deletions components/app/R/modules/AuthenticationModule.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -220,7 +220,7 @@ FirebaseAuthenticationModule <- function(input, output, session)
new(persistence = "local")

observeEvent(input$launchGoogle, {
firebase$launch_google()
firebase$launch_google(flow = "popup")
})

resetUSER <- function() {
Expand Down Expand Up @@ -628,7 +628,7 @@ splashLoginModal <- function(ns=NULL, with.email=TRUE, with.password=TRUE,
titles[[11]] = c("Zoom-zoom-insight!","Get faster insight from your data")
titles[[12]] = c("Click-click-eureka!","Owe yourself that <i>eureka!</i> moment")
titles[[13]] = c("I Love Omics Data!","Unleash your inner nerd with BigOmics Playground")
titles[[14]] = c("More Omics Data","Is all I want for Christmas")
titles[[14]] = c("More Omics Data","Is all I want for my birthday")
titles[[15]] = c("Keep Exploring","Never stop discovering with BigOmics Playground")
titles[[16]] = c("Real Bioinformaticians","Do it with BigOmics Playground")
titles[[17]] = c("Real Biologists","Do it with BigOmics Playground")
Expand Down
1 change: 0 additions & 1 deletion components/app/R/modules/MakeContrastModule.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -453,7 +453,6 @@ MakeContrastServerRT <- function(id, phenoRT, contrRT, countsRT, height=720)


pcaplot.RENDER <- shiny::reactive({
##ngs <- inputData()
##X <- ngs$X
pheno <- phenoRT()
counts <- countsRT()
Expand Down
50 changes: 38 additions & 12 deletions components/app/R/modules/WelcomeBoard.R
View file
Original file line number Diff line number Diff line change
@@ -1,23 +1,24 @@
##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2022 BigOmics Analytics Sagl. All rights reserved.
## Copyright (c) 2018-2023 BigOmics Analytics Sagl. All rights reserved.
##

WelcomeBoard <- function(id, auth) {}
WelcomeBoardInputs <- function(id) {}
WelcomeBoardUI <- function(id) {}


WelcomeBoard <- function(id, auth, r_global) {
WelcomeBoard <- function(id, auth, enable_upload, r_global) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE

output$welcome <- shiny::renderText({
name <- auth$name()
dbg("[WelcomeBoard] name =",name)
if (name %in% c("", NA, NULL)) {
welcome <- "Welcome back..."
} else {
first.name <- strsplit("ivo kwee", split = "[@ .]")[[1]][1]
first.name <- strsplit(name, split = "[@ .]")[[1]][1]
first.name <- paste0(
toupper(substring(first.name, 1, 1)),
substring(first.name, 2, nchar(first.name))
Expand All @@ -28,8 +29,34 @@ WelcomeBoard <- function(id, auth, r_global) {
})

observeEvent(input$init_example_data, {
r_global$load_example_trigger <- TRUE
r_global$load_example_trigger <- r_global$load_example_trigger +1
})

observeEvent(input$init_upload_data, {
if(enable_upload) {
bigdash.openSidebar()
bigdash.selectTab( session, "upload-tab" )
} else {
shinyWidgets::sendSweetAlert(
session = session,
title = "Upload disabled",
text ='Sorry, upload of new data is disabled for this account.',
type = "warning",
btn_labels = "OK",
closeOnClickOutside = FALSE
)
}
})

observeEvent(input$init_load_data, {
# close the right sidebar
shinyjs::runjs("$('#settings-container').trigger('click');")
shinyjs::runjs("$('#settings-container').trigger('mouseleave');")

bigdash.openSidebar()
bigdash.selectTab( session, "load-tab" )
})

})
}

Expand All @@ -39,7 +66,6 @@ WelcomeBoardInputs <- function(id) {

WelcomeBoardUI <- function(id) {
ns <- shiny::NS(id) ## namespace

div(
id = "welcome-page",
br(),
Expand All @@ -57,21 +83,21 @@ WelcomeBoardUI <- function(id) {
h3("I am new..."),
shiny::actionButton(
ns("init_example_data"),
label = "Try example dataset",
label = "Load example dataset",
class = "btn btn-outline-info welcome-btn"
)
),
div(
class = "col-md-7",
h3("I'm an existing user..."),
tags$a(
id = "init-upload-data",
"Upload new data",
shiny::actionButton(
ns("init_upload_data"),
label = "Upload new data",
class = "btn btn-outline-info welcome-btn"
),
tags$button(
id = "init-load-data",
"Use my saved data",
shiny::actionButton(
ns("init_load_data"),
label = "Use my saved data",
class = "btn btn-outline-primary welcome-btn"
)
)
Expand Down
Loading

0 comments on commit da98222

Please sign in to comment.