dms-viz/dms-viz.github.io issues and pull requests

#99 - plot sum or mean of absolute value of a metric

Issue - State: open - Opened by jbloom 22 days ago

#98 - Ameliorate lag in the legend UI

Pull Request - State: closed - Opened by WillHannon-MCB 9 months ago

#97 - be able to select just one condition to show lineplot for

Issue - State: closed - Opened by jbloom 9 months ago - 5 comments

#96 - the `--description` option is broken

Issue - State: closed - Opened by jbloom 9 months ago - 1 comment

#95 - problems with select all for large structures

Issue - State: open - Opened by jbloom 10 months ago - 2 comments

#94 - Network error loading protein structures from the RCSB

Issue - State: closed - Opened by WillHannon-MCB about 1 year ago
Labels: bug

#93 - Fix Consortium author

Pull Request - State: closed - Opened by csoneson about 1 year ago

#92 - Fix bug with `floor` when switching datasets

Pull Request - State: closed - Opened by WillHannon-MCB about 1 year ago

#91 - Floored effect coloring sometimes is carried over between datasets

Issue - State: closed - Opened by Caleb-Carr about 1 year ago - 2 comments

#90 - hyperlinks in Markdown description not colored

Issue - State: closed - Opened by jbloom about 1 year ago - 2 comments

#89 - Menu state takes priority over the default values in the config file

Issue - State: closed - Opened by WillHannon-MCB about 1 year ago

#88 - Enable the heatmap's color scale to be non-symmetric with custom center and range

Pull Request - State: closed - Opened by WillHannon-MCB about 1 year ago

#87 - Fix issues with state change between datasets

Pull Request - State: closed - Opened by WillHannon-MCB about 1 year ago

#86 - Issues with state between datasets

Issue - State: closed - Opened by WillHannon-MCB about 1 year ago
Labels: bug

#85 - Color for wild-type score

Issue - State: closed - Opened by afrubin about 1 year ago - 1 comment

#84 - Docs typo?

Issue - State: closed - Opened by jgallowa07 about 1 year ago - 1 comment

#83 - Overhaul CSS and UI components

Pull Request - State: closed - Opened by WillHannon-MCB over 1 year ago

#82 - documentation mentions a component called `dms-view`, but i can't find a reference to this anywhere

Issue - State: closed - Opened by WillHannon-MCB over 1 year ago - 1 comment

#81 - consistent color coding between the line plot and 3D visualization to improve user understanding/mapping to colors

Issue - State: closed - Opened by WillHannon-MCB over 1 year ago - 1 comment

#80 - One of the data points is highlighted by a larger black circle, can you explain what the significance of this data point is and its relation to the other visualizations?

Issue - State: closed - Opened by WillHannon-MCB over 1 year ago - 1 comment

#79 - Add support for insertion codes

Pull Request - State: closed - Opened by WillHannon-MCB over 1 year ago

#78 - Support non-numeric sites in the PDB

Issue - State: closed - Opened by WillHannon-MCB over 1 year ago - 1 comment

#77 - Convert 'Site All Sites' checkbox to a button

Pull Request - State: closed - Opened by WillHannon-MCB over 1 year ago

#76 - Add median as summary statistic

Pull Request - State: closed - Opened by WillHannon-MCB over 1 year ago

#75 - Check for new releases before deploying to GitHub Pages

Pull Request - State: closed - Opened by WillHannon-MCB over 1 year ago

#74 - Add default filters

Issue - State: closed - Opened by afrubin over 1 year ago - 1 comment

#73 - Add median score

Issue - State: closed - Opened by afrubin over 1 year ago - 1 comment

#72 - Reset structure doesn't work?

Issue - State: closed - Opened by afrubin over 1 year ago - 1 comment

#71 - Select All Sites should be a button

Issue - State: closed - Opened by afrubin over 1 year ago - 1 comment

#70 - Filter options is blank in the example dataset?

Issue - State: closed - Opened by afrubin over 1 year ago - 1 comment

#69 - Color options

Issue - State: closed - Opened by afrubin over 1 year ago - 1 comment

#68 - Include meta tags in the HTML, especially for description and title

Issue - State: closed - Opened by WillHannon-MCB over 1 year ago - 1 comment

#67 - Also consider displaying the app version on the browser, helps users and developers debug issues

Issue - State: closed - Opened by WillHannon-MCB over 1 year ago - 1 comment

#66 - Separate development and deployment into separate workflows

Issue - State: closed - Opened by WillHannon-MCB over 1 year ago - 1 comment

#65 - I would suggest separating the application code from its deployment to github pages; the repo can get crowded once there are multiple versions (v0 directories)

Issue - State: closed - Opened by WillHannon-MCB over 1 year ago - 1 comment

#64 - Consider placing key interaction instructions above the plots for better user guidance

Issue - State: closed - Opened by WillHannon-MCB over 1 year ago - 1 comment

#63 - minimize and help icons are off the sidebar

Issue - State: closed - Opened by WillHannon-MCB over 1 year ago - 1 comment

#62 - Some of the sections in the chart options are helpful to understand the visualization itself, for example, the legend for antibody or the toggle to display mutational counts

Issue - State: closed - Opened by WillHannon-MCB over 1 year ago - 1 comment

#61 - Expanding filter sites from the left sidebar doesn't show anything for the default example (wasn't sure how that gets populated), if there are no filters, let the user know

Issue - State: closed - Opened by WillHannon-MCB over 1 year ago - 1 comment

#60 - Explore the option of automatically focusing the protein viewer when clicking on a data point

Issue - State: closed - Opened by WillHannon-MCB over 1 year ago - 1 comment

#59 - Provide tooltips to explain the line plots on top and the interactions, especially for users lacking domain knowledge in protein space

Issue - State: closed - Opened by WillHannon-MCB over 1 year ago - 1 comment

#58 - Review for JOSS

Issue - State: closed - Opened by jkanche over 1 year ago - 2 comments

#57 - Unset Default Filter Values Reset on Dataset Change Leading to Inaccurate Visualizations

Issue - State: closed - Opened by WillHannon-MCB over 1 year ago
Labels: bug

#56 - Accomodate markdown descriptions in the `.json` specification

Pull Request - State: closed - Opened by WillHannon-MCB almost 2 years ago

#55 - Optionally provide markdown descriptions in the JSON specification

Issue - State: closed - Opened by WillHannon-MCB almost 2 years ago
Labels: enhancement

#54 - Allow users to select points on the protein by clicking in the focus plot

Pull Request - State: closed - Opened by WillHannon-MCB almost 2 years ago

#53 - Allow users to select points on the protein by clicking

Issue - State: closed - Opened by WillHannon-MCB almost 2 years ago
Labels: enhancement

#52 - Add filtering step to `protein.updateData()`

Pull Request - State: closed - Opened by WillHannon-MCB almost 2 years ago

#51 - Protein color scale isn't changing when filters are applied

Issue - State: closed - Opened by WillHannon-MCB almost 2 years ago
Labels: bug

#50 - Change the default summary metric to the average at each site

Issue - State: closed - Opened by WillHannon-MCB almost 2 years ago

#49 - Change the default dataset to something more meaningful

Issue - State: closed - Opened by WillHannon-MCB almost 2 years ago
Labels: documentation

#48 - Show all non-carbon hydrogens

Pull Request - State: closed - Opened by WillHannon-MCB almost 2 years ago

#47 - Add nucleotide representation and bond order

Pull Request - State: closed - Opened by WillHannon-MCB almost 2 years ago

#46 - Show all non-carbon hydrogens

Issue - State: closed - Opened by WillHannon-MCB almost 2 years ago
Labels: enhancement

#45 - Add bond orders to the structures

Issue - State: closed - Opened by WillHannon-MCB almost 2 years ago
Labels: enhancement

#44 - Strange protein representation

Issue - State: closed - Opened by WillHannon-MCB almost 2 years ago
Labels: help wanted, question

#43 - More sensible color scale domain

Issue - State: closed - Opened by WillHannon-MCB almost 2 years ago
Labels: bug

#42 - Add a more sensible default for flooring the data

Issue - State: closed - Opened by WillHannon-MCB almost 2 years ago
Labels: enhancement

#41 - Add markdown description

Pull Request - State: closed - Opened by WillHannon-MCB almost 2 years ago

#40 - Add optional bounds to the filters

Issue - State: closed - Opened by WillHannon-MCB almost 2 years ago
Labels: enhancement

#39 - Add a global description

Issue - State: closed - Opened by WillHannon-MCB almost 2 years ago
Labels: enhancement

#38 - Make it possible to set the negative color

Issue - State: closed - Opened by WillHannon-MCB almost 2 years ago
Labels: enhancement

#37 - Implement versioning using routes

Issue - State: closed - Opened by WillHannon-MCB almost 2 years ago - 2 comments
Labels: enhancement

#36 - Add optional titles to the main plot

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: enhancement

#35 - Add a coloring option for ligands to show individual molecules

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: enhancement

#34 - The initial size of the protein isn't correctly determined on page load

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago - 1 comment
Labels: bug

#33 - Change the numbering on the structure tooltip

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: bug

#32 - Add more structure representations to the tool

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: enhancement

#31 - Structure should reload if dataChains are different between datasets

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: bug

#30 - Wildtype amino acid label issue in certain datasets

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: bug

#29 - Add user defined descriptions for each experiment

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago - 1 comment
Labels: enhancement

#28 - Replace color inversion with color complement

Pull Request - State: closed - Opened by WillHannon-MCB about 2 years ago

#27 - Fix color inversion for negative effects

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: bug

#26 - Allow to choose epitope colors

Issue - State: closed - Opened by Bernadetadad about 2 years ago - 5 comments
Labels: documentation

#25 - Download pdb file

Issue - State: closed - Opened by Bernadetadad about 2 years ago - 1 comment
Labels: enhancement

#24 - Generalize epitope requirement

Pull Request - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: enhancement

#23 - Error can prevent chart from rendering with combinations of filters

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: bug

#22 - Write detailed documentation with tutorials

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago - 2 comments
Labels: documentation

#21 - Improve error handling and notifications

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: enhancement

#20 - Dynamically resize the y-axis tick labels

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: bug

#19 - Add media queries for tooltip size

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: enhancement

#18 - The URL isn't correctly setting the state of the Protein Option sliders

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: bug

#17 - Fix the initial status of the sidebar based on page width

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: bug

#16 - Add a button to save the plot as a PNG image

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago - 1 comment
Labels: enhancement

#15 - Provide a summary of the number of measurements at each site

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: enhancement

#14 - Optionally exclude certain mutations from the site summary statistic

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago
Labels: enhancement

#13 - Remove the requirement for 'epitopes' in the input data

Issue - State: closed - Opened by WillHannon-MCB about 2 years ago - 1 comment
Labels: enhancement

#12 - Add url state management

Pull Request - State: closed - Opened by WillHannon-MCB about 2 years ago

#11 - View multiple epitopes

Pull Request - State: closed - Opened by WillHannon-MCB about 2 years ago

#10 - Add point deselection

Pull Request - State: closed - Opened by WillHannon-MCB over 2 years ago

#9 - Add point deselection with a hot key

Issue - State: closed - Opened by WillHannon-MCB over 2 years ago
Labels: enhancement

#8 - Heatmap tooltip gets cut off at the top of the chart

Issue - State: closed - Opened by WillHannon-MCB over 2 years ago - 1 comment
Labels: bug

#7 - link dms-viz and configure_dms-viz pages

Issue - State: closed - Opened by Bernadetadad over 2 years ago
Labels: documentation

#6 - Integrate with dms-vep pipeline

Issue - State: closed - Opened by Bernadetadad over 2 years ago - 1 comment
Labels: enhancement

#5 - smaller line plots

Issue - State: closed - Opened by Bernadetadad over 2 years ago
Labels: enhancement

#4 - Amino acid single letter code

Issue - State: closed - Opened by Bernadetadad over 2 years ago - 1 comment
Labels: enhancement

#3 - Keep track of protein structure coordinates

Issue - State: closed - Opened by Bernadetadad over 2 years ago - 1 comment
Labels: enhancement

#2 - viz instructions

Issue - State: closed - Opened by Bernadetadad over 2 years ago - 2 comments
Labels: enhancement

#1 - Broken link

Issue - State: closed - Opened by Bernadetadad over 2 years ago - 1 comment

GitHub / dms-viz/dms-viz.github.io issues and pull requests