CHANGELOG.md

1.5.12

• Bugfix for plot cluster coloring
• More appropriate cluster bounding given color scheme

1.5.11

• Fix button alignment
• Add pseudocells.R informational file

1.5.10

• Fix Pseudocell Help popup not popping up on second+ activation

1.5.9

• Add pseudocell popup instructions
• Additional notation on optional, required uploads

1.5.8

• Fix low dim visualization plotting bug
• Update download function

1.5.7

• eventReactive bugfix on get_data that caused crashing when no correspondence matrix was uploaded and use_boma flag was false
• Fix error on modifying clustering after changing dimension by removing dependence on input$d

1.5.6

• Small formatting fixes/tweaks

1.5.5

• Added more color options
• Fixed small bug for statistics with action buttons
• Styling changes
• UI changes to correspond with figure

1.5.4

• Added a run button
• Removed boma folder
• Reorganize functions
• Revise UI on uploads

1.5.3

• Add color theme selector
• Add higher resolution figure 1
• Add slider for global alignment KNN
• Filter pseudocell datasets
• Rearrange UI to be more intuitive

1.5.2

• UI changes
• More user explanations
• Dataset renaming and filtering
• BOMA ordering bugfix
• Added KNN method for local alignment
• Automatically detect genes in common between datasets

1.5.1

• UI changes
• Dataset uploads
• Dataset size reductions
• Common gene detection

1.5.0

• Add better dataset annotations
• Add figure
• Add more datasets
• Added preprocess.R for adding datasets more easily
• Better error handling for statistics
• More error catching for sample datasets
• Various UI changes and fixes

1.4.0

• Helper text revisions
• Implement pairwise distance
• Implement quick dataset loading framework
• Legend changes
• Moved distance heatmap
• Properly implement BOMA sorting method
• Properly implement DTW method
• Revised and compressed layout

1.3.12

• BOMA rough implementation
• Fix UI bugs

1.3.11

• Add BOMA UI framework and reactive elements

1.3.10

• Add color bar and unfinished integrated application
• Revise certain UI elements
• Add runtime warnings

1.3.9

• Initial direction/scale of plots same
• Switch default to 'time'
• Add 'color' annotation to series selection
• Remove medoids bar
• Add link to download base dataset
• Error catching

1.3.8

• Added compatibility for ShinyApps.io

1.3.7

• Uploaded default data

1.3.6

• Added movable plots
• Transitioned main plots to plotly

1.3.5

• Added heatmap labels
• Various UI updates
• Better accuracy barplot formatting
• Fixed cluster coloration bug
• Added BOMA checkbox, still needs full implementation

1.3.4

• Change UI text
• Code optimization
• Fixed legend title bug
• Fix startup errors
• Add indication for alignments in progress
• Move default data read to somewhere more appropriate
• Update helper UI icons
• Directory reorganization
• Uploaded raw svg for icons

1.3.3

• Removed upload/download size limitation
• Update README.md with minimal usage instructions

1.3.2

• Remove time default coloring
• Add dynamic selection of coloring column in metadata
• Code cleanup

1.3.1

• Remove None clustering
• Add www folder
• Add helping images
• Additional metadata error analysis and flexibility
• Added bar plot for label transfer accuracy

1.3.0

• Clustering visualization fix
• Visualization QOL updates
• UI and UX changes (including terminology, coloration, and labeling)
• Added optional clustering visualization for Scatter3D
• Update downloaded information

1.2.0

• Add heatmap visualizing cross-modal clusters
• QOL UI improvements
• Spectral cluster framework
• Added placeholder for gene outcomes

1.1.1

• 3D graph label bugfix

1.1.0

• More QOL notes and default changes
• Enhanced explanations
• Spread out UI
• Visualization clustering section added with K-Means and PAM methods
• Optional label transfer accuracy calculation added

1.0.0

• Initial Release
• Main UI, dynamic parameter selection, basic upload/download