Dev#22

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Tsarin2061 wants to merge 215 commits into

ostash-group:devfrom

Commits on Jan 25, 2021

Added docsify quick guide and introduction. Added more example data
Pavlo Hrab
committed

Commits on Jan 26, 2021

Added upload example data buttons
Pavlo Hrab
committed
Deleted arbitrary files
Pavlo Hrab
committed
Simplified README
Pavlo Hrab
committed
Added biocircos image
Pavlo Hrab
committed

Commits on Jan 31, 2021

Fixed example ARTS data upload bug
Pavlo Hrab
committed
Default chr length is now 10 Mbp
Pavlo Hrab
committed
Renamed Data manipulation options menu
Pavlo Hrab
committed
Completed the documentation
Pavlo Hrab
committed
Delete .~lock.antismash_1.csv#
Pavlo Hrab
authored
Deleted obsidian workspace junk folder
Pavlo Hrab
committed
Renamed the renaming scheme upload field
Pavlo Hrab
committed
Deleted obsolete image files
Pavlo Hrab
committed
Fixed the shiny app link in README
Pavlo Hrab
authored
Merge pull request #2 from ostash-group/dev
Pavlo Hrab
authored
Update README.md
Pavlo Hrab
authored

Commits on Feb 2, 2021

Merge pull request #1 from ostash-group/master
Pavlo Hrab
authored
Added badges
Pavlo Hrab
authored
Merge pull request #3 from pavlohrab/master
Pavlo Hrab
authored

Commits on Feb 3, 2021

Replaced IntervalSurgeon with GRanges
Pavlo Hrab
committed
Merge pull request #4 from pavlohrab/master
Pavlo Hrab
authored

Commits on Mar 8, 2021

Changed link to an app
Pavlo Hrab
authored
Changed link for an app
Pavlo Hrab
authored
Changed link to an app
Pavlo Hrab
authored
Merge pull request #2 from ostash-group/master
Pavlo Hrab
authored

Commits on May 17, 2021

Fixed weird issue when hexadecimal numbers were converted to integers in $biocircos and $biocircos_legend
pavlohrab
committed

Commits on May 24, 2021

Integrated gecco
Pavlo
committed

Commits on May 28, 2021

Rewrote core computations + many if statements in for loops
Pavlo
committed
Added example gecco data
Pavlo
committed

Commits on Jul 10, 2021

Last stable working version. Refractored the code.
Pavlo Hrab
committed

Commits on Jul 11, 2021

Added comments, deleted testing chunks
Pavlo Hrab
committed
DeepBGC and GECCO data do not crashe
Pavlo Hrab
committed
Merge pull request #5 from pavlohrab/dev
Pavlo Hrab
authored

Commits on Oct 7, 2021

Removed shiny library() statement, made ::
Pavlo Hrab
committed
Removed BioCircos library() statement, made ::
Pavlo Hrab
committed
Removed tidyverse library() statement, made :: for tidyr, plyr and dplyr
Pavlo Hrab
committed
Removed DT library() statement, made ::
Pavlo Hrab
committed
Removed ggplot2 library() statement, made ::
Pavlo Hrab
committed
Removed plotly library() statement, made ::
Pavlo Hrab
committed
Removed shinyjs library() statement, made ::
Pavlo Hrab
committed
Removed rjson library() statement, made ::
Pavlo Hrab
committed
Removed stringr library() statement, made ::
Pavlo Hrab
committed
Removed GenomicRanges library() statement, made ::
Pavlo Hrab
committed

Commits on Oct 8, 2021

data_uploads and similar lists used for iteration in app made global
Pavlo Hrab
committed
GECCO ref comparison have full text description, not letter coding. update_ui_with_data is introduced
Pavlo Hrab
committed
Created reading functions for every type of input
Pavlo Hrab
committed

Commits on Oct 9, 2021

Fixed RRE data loading and visualization bug
Pavlo Hrab
committed
Fixed duplicates function now is fixing duplicates. This solved PRISM json upload bug
Pavlo Hrab
committed
Fixed duplicates function one more time. Works as expected
Pavlo Hrab
committed
Added accept value to fileInput fields
Pavlo Hrab
committed
Accept value now gathers json file for prism and antismash
Pavlo Hrab
committed
Added MIME type detection for antismash and prism data
Pavlo Hrab
committed
Add Start-Stop columns for DeepBGC data
Pavlo Hrab
committed
input now code names, not letters
Pavlo Hrab
committed
Fix RRE not coloring bug
Pavlo Hrab
committed
Deleted soft_let list used for coding. Now only abbr is used
Pavlo Hrab
committed

Commits on Oct 10, 2021

Use of datatable for coloring, not the dataframe
Pavlo Hrab
committed
biocircos_legend datatable is now editable from shiny
Pavlo Hrab
committed

Commits on Oct 11, 2021

Gecco data comparison ui is now not loading untill comparable dataframe is uploaded
Pavlo Hrab
committed
DeepBGC data comparison ui is now not loading untill comparable dataframe is uploaded
Pavlo Hrab
committed
Fix deep_reference plotting error, when reference data is empty
Pavlo Hrab
committed
Fix input is not hiding after input is triggered
Pavlo Hrab
committed
Fix input and input trigger Biocircos replotting
Pavlo Hrab
committed
Added warning that hybrid settings are resseted after reset names for Antismash, PRISM and SEMPI
Pavlo Hrab
committed
Fix plots weren't loading at fresh app startup
Pavlo Hrab
committed
Fixed previous commit: added different triggers to inputData to trigger enable_event_logic
Pavlo Hrab
committed
Add prodigiosin as other to the rename.csv
Pavlo Hrab
committed
Fix arts_data_input increment (ARTS SCO data was not laoding correctly)
Pavlo Hrab
committed
Fix prism_supp_data ID adding based on Start of gene (in ascending order)
Pavlo Hrab
committed
Fix edit of vals trigger Biocircos replotting
Pavlo Hrab
committed
Fix PRISM-Supp checkbox. Now data can be hidden from plots
Pavlo Hrab
committed
Add basic debouncing for dynamicIutput
Pavlo Hrab
committed

Commits on Oct 12, 2021

Added debouncing for DeepBGC and GECCO filtering. Decreased reactivity of deep_reference, by puting calculation into observeEvent
Pavlo Hrab
committed
Add input data validation for antismash, prism and sempi
Pavlo Hrab
committed
Add RRE input data validation
Pavlo Hrab
committed

Commits on Oct 19, 2021

Initial dashboard working prototype
Pavlo Hrab
committed

Commits on Oct 20, 2021

Added scrollbars to group_by table
Pavlo Hrab
committed
Fix box resizebility. Also added heigth = 100%
Pavlo Hrab
committed
Fix DeepBGC and Gecco filtering boxes showing after data upload
Pavlo Hrab
committed
Added icons for sidebar
Pavlo Hrab
committed

Commits on Oct 26, 2021

Added loaders, DeepBGC data validation and disconnect message
Pavlo Hrab
committed
Added DeepBGC filtering to the sidebar
Pavlo Hrab
committed
Fixed icons for DeepBGC menuItems
Pavlo Hrab
committed
Added GECCO filtering to the sidebar
Pavlo Hrab
committed
Sidebar is not reorderable, but looks better
Pavlo Hrab
committed

Commits on Oct 29, 2021

Move validation functions to a separate file
Pavlo Hrab
committed

Commits on Oct 30, 2021

Move helper functions to a separate file
Pavlo Hrab
committed
Add close action to boxes and restore button
Pavlo Hrab
committed

Commits on Nov 1, 2021

move biocircos, deep_reference and group_rable functions into separate files
Pavlo Hrab
committed
Add draggable events for Annotation on chromosome and group_table plots
Pavlo Hrab
committed
boxes are now resizable only in 2 direction
Pavlo Hrab
committed
Added box sidebar for Biocircos plot
Pavlo Hrab
committed
Remove draggable events (interfere with plotly select events)
Pavlo Hrab
committed
Annotation on chromosome plots are in column layout now
Pavlo Hrab
committed
Add Improve visualization box hiding if no data, that is used, were uploaded
Pavlo Hrab
committed
Add prism_supplement_arts_box hiding if no data, that is used, were uploaded
Pavlo Hrab
committed
Fixed DeepBGC filtering
Pavlo Hrab
committed

Commits on Nov 2, 2021

Add global filtering values to compare. Filtering can be done right from sidebar
Pavlo Hrab
committed
Fix filtering value change after initial UI rendering, if in another place they have been changed
Pavlo Hrab
committed
Add column-based global options layout. Boxes there are not resizable now
Pavlo Hrab
committed
Fix app hanging on window close
Pavlo Hrab
committed

Commits on Nov 3, 2021

Initial commit of golem-structured app
Pavlo Hrab
committed

Commits on Nov 4, 2021

Read example data should work now
Pavlo Hrab
committed
Refined reading example data from package
Pavlo Hrab
committed
Pipe operator should not be exported
Pavlo Hrab
committed
Fixed .gitignore file
Pavlo Hrab
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Export tranformation to csv function. Fixed package structure
Pavlo Hrab
committed

Commits on Nov 5, 2021

Added deep_reference plot module
Pavlo Hrab
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Add deep_reference_2 module
Pavlo Hrab
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Add barplot_rank module
Pavlo Hrab
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Add group_table module
Pavlo Hrab
committed
Add download module
Pavlo Hrab
committed
Add deepbgc_plots module
Pavlo Hrab
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Add gecoo_plots module
Pavlo Hrab
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Add biocircos module
Pavlo Hrab
committed

Commits on Feb 17, 2022

Fixed sco_rre loading
pavlohrab
committed

Commits on May 27, 2022

Commits on May 28, 2022

Commits on Jun 1, 2022

R cmd check 'no visible bindings' error resolved
pavlohrab
committed

Commits on Jun 2, 2022

Commits on Jun 3, 2022

Commits on Jun 4, 2022

Commits on Jul 29, 2022

Added dissect.py script and documentation
pavlohrab
committed

Commits on Sep 5, 2022

Merge pull request #14 from pavlohrab/master
pavlohrab
authored

Commits on Oct 19, 2022

removed column other&other_probability in gecco data processing stage
Tsarin2061
committed

Commits on Feb 14, 2023

adding rawdata as ripp_data-requires changing path to file; file with RiPPMiner data itself.R; Action button for user data and example data; Read_ripp in fct_reading_functions.R; Processing of ripp…
Tsarin2061
committed

Commits on Feb 19, 2023

changed URLs in data-raw,fixed 'misleading code' in data-raw
Tsarin2061
committed

Commits on Feb 23, 2023

Commits on Feb 24, 2023

RippMiner: processing user data
Tsarin2061
committed

Commits on Mar 12, 2023

fully functional RippMiner-genome analysis
Tsarin2061
committed

Commits on Sep 20, 2023

ARTS tree sidemenu created
LevTsarin
committed

Commits on Sep 26, 2023

WIP
LevTsarin
committed

Commits on Oct 10, 2023

Commits on Oct 11, 2023

Commits on Oct 13, 2023

fixing tree object
LevTsarin
committed

Commits on Oct 14, 2023

Commits on Oct 23, 2023

Emerald/Santiss working, no deep testing performed
LevTsarin
committed

Commits on Nov 28, 2023

Commits on Dec 8, 2023

Commits on Dec 9, 2023

bug fixes
LevTsarin
committed