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Clusters app v1.2 update #33

Merged
merged 103 commits into from
Jul 12, 2021
Merged

Clusters app v1.2 update #33

merged 103 commits into from
Jul 12, 2021

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bhavyaac
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@bhavyaac bhavyaac commented Jun 22, 2021 •
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List of changes below, all have been tested on the server:

CooberHoo and others added 15 commits June 17, 2021 09:46
@CooberHoo
added cluster labels to clustering tab, added different clustering op…
dde6f22 
…tions, changed download type to pdf
@CooberHoo
Updated info/instructions for each tabs
6c0cf36
@CooberHoo
added toggleable labels on dimension reduction plots, turned network …
0c75cab 
…visualisation to plotly -pending further work to make it more interactive
@bhavyaac
Adjust gene label alignment, disable scroll for bubble plots
c75f327
@bhavyaac
Remove TODO for closed issue
cd65cc7
@CooberHoo
added very basic hovering to network visualisation, added server side…
b504df3 
… book marking, added custom styling (issue: braindex image not displayed)
@bhavyaac
Implement bookmark button beside update button
ae78b81
@bhavyaac
Enable url-based bookmarking
352e0fc
@bhavyaac
Streamline loading spinner code using ui_functions file
94c7d51
@CooberHoo
added serverside bookmarking, custom formatting
aaf1580
@CooberHoo
removed shiny_bookmarks
d07c82e
@bhavyaac
Switch to server-side bookmarking - issue #28 (only tested locally)
0e020e4
@bhavyaac
Match expression table column order to bubble plots - issue #16
b69f8e7
@bhavyaac
Add toggle for displaying mean expression to table tab, edit docs
6efbe7e
@bhavyaac
Show number of cells in timecourse tooltip - issue #19
3ba70d4
@bhavyaac bhavyaac changed the title Big fix & small enhancements to v1.1 Bug fix & small enhancements to v1.1 Jun 22, 2021
bhavyaac and others added 14 commits June 22, 2021 18:20
@bhavyaac
Add code documentation for new sections
af435f5
@bhavyaac
Alter timecourse tooltip text and plotly controls
66dcd10
@bhavyaac
Create new tab to to rank clusters by expression - issue #20
4b3b6c8
@CooberHoo
modified labels, tool-tips, legends, comments
c033cfd
@CooberHoo
commented out code that doesn't work yet
a429370
@CooberHoo @sjessa
added cluster labels to clustering tab, added different clustering op…
f32749d 
…tions, changed download type to pdf
@CooberHoo @sjessa
Updated info/instructions for each tabs
32c2b1c
@CooberHoo @sjessa
added toggleable labels on dimension reduction plots, turned network …
188fbb1 
…visualisation to plotly -pending further work to make it more interactive
@CooberHoo @sjessa
added very basic hovering to network visualisation, added server side…
a87472f 
… book marking, added custom styling (issue: braindex image not displayed)
@CooberHoo @sjessa
added serverside bookmarking, custom formatting
6506d55
@CooberHoo @sjessa
removed shiny_bookmarks
cc1175b
@CooberHoo @sjessa
modified labels, tool-tips, legends, comments
083e940
@CooberHoo @sjessa
commented out code that doesn't work yet
539afc4
@sjessa
Merge branch 'dev_howard' of github.com:fungenomics/braindex into dev…
6dc1fd6 
…_howard
bhavyaac and others added 24 commits July 12, 2021 12:25
@bhavyaac
Include shiny_bookmarks folder in .gitignore
a271f87
@bhavyaac
Implement file upload (csv or tsv only) for gene lists
dab8c7e
@bhavyaac
Allow user to use the textbox only, file upload optional - issue #17
e2b0a9a
@bhavyaac
Toggle spike lines on by default for timeseries interactive plot
d3c262a
@bhavyaac
Display mean expression toggle for <2 genes in textbox
78bbdcc
@bhavyaac
Remove user toggle for spikelines in timecourse interactive plot
532d17d
@bhavyaac
Toggle between file upload and textbox input for gene selection - issue
b676c02 
#17
@bhavyaac
Update text in file upload function + error message
fd31c1c
@bhavyaac
Switch back to conditionally displaying mean expression toggle
2c0bf7b
@bhavyaac
Alter docs and sidebar formatting to match GRN app
74e30f9
@bhavyaac
Switch back to URL bookmarking
d90cf68
@bhavyaac
Add mean expression toggle to ranked clusters tab, alter plot formatting
77db434
@bhavyaac
Clarify expression vs. proportion in ranked clusters tab
f424262
@bhavyaac
Implement expression table with reactable, alter text color in dark b…
7543aa1 
…ackground - issue #32
@bhavyaac
Load reactable package, comment out DT package
028f577
@bhavyaac
Display error message for genes in uploaded files that aren't in data…
4091e50 
…set - issue #17
@bhavyaac
Remove case sensitivity for gene input error messages - issue #17
69aff40
@bhavyaac
Revert "Remove case sensitivity for gene input error messages - issue #…
23e9d9a 
…17"

This reverts commit 6918850.
@bhavyaac
Extract part of input validation step to a function - issue #37
ef4d939
@bhavyaac
Add dropdown menu to choose between inputs in timecourse tab - issue #38
6b4b3ad
@bhavyaac
Adjust app formatting during server test
a683453
@bhavyaac
Adjust formatting and remove sticky column in table (server testing)
17e9d78
@bhavyaac
Adjust formatting and alignment of dendrogram and table tabs (server …
f3446a8 
…testing)
@bhavyaac
Adjust formatting and alignment (server testing)
d4912a4
@bhavyaac bhavyaac marked this pull request as ready for review July 12, 2021 16:26
@bhavyaac bhavyaac merged commit a442582 into master Jul 12, 2021
@bhavyaac bhavyaac changed the title Bug fix & enhancements to v1.1 Bug fix & enhancements to v1.1 clusters app Jul 30, 2021
@bhavyaac bhavyaac changed the title Bug fix & enhancements to v1.1 clusters app Clusters app v1.2 update Nov 19, 2021
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@bhavyaac @CooberHoo @sjessa