a quick disclaimer: this is unfinished software! Things may be funky/broken/unintuitive. Thanks in advance for your time, patience, and infinitely helpful feedback.
From your local anvi'o codebase, run git checkout genomeview-backend to pull + sync the remote genomeview-backend branch.
Genome View relies on an additional submodule called Fabric.js . We can make sure we have that by running
git submodule update --init
You should now be able to run anvi-self-test --suite genome-view without any hiccups. Open the resultant URL in Chrome, and lets go!
- The 'main canvas' - this is where your visualization lives
- The 'nav bar' - your one stop shop for quickly navigating the main canvas
- The 'settings pane' - an anvi'o classic! Easily accessible with the
sshortcut
Manually navigating the main canvas can happen in a few different ways.
- Mousewheel up/down over the main canvas will zoom in/out
- Manipulating the nav bar (slide, condense, expand) will adjust the main canvas accordingly
- Supplying start/stop values for the input fields on the bottom left of the nav bar, followed by
enter - Clicking the
+and-buttons on the bottom right of the nav bar will zoom in/out - The main canvas also has a verticle scrollbar of its own to view obscured genome groups
Genome View offers two main avenues for gene-level information
- The 'ephemeral tooltip', available by hovering over a gene arrow
- The 'deepdive tooltip', available by clicking on a gene arrow
Go ahead and mouse over any gene in the main canvas
- Is all the expected information rendered in the tooltip?
- Is the rendered data laid out sensibly?
Now, click on any gene to open the deepdive tooltip
- Is it immediately clear what additional information/UI is exposed here?
- Try blasting a gene - is this feature functioning as expected?
While we have the deepdive tooltip open, let's explore metadata
- Metadata is divided into two categories
- tags - for short, keyword descriptors
- descriptions - for longer, more thorough text associated with a given gene.
- Add a test metadata tag to a handful of arbitrary genes. I like to use 'cats' :)
- Your tags should immediately populate the metadata section of the tooltip
- You can query for tags against the entire sequence and instantly see your hits
- In the metadata section, click "Query Sequence for Matches" for a given tag
- Your visualization should:
- zoom out to a depth containing all hits
- glow each matched gene in the visualization for 5 seconds*
- *the glow effect is slightly broken right now ;)
- You can also query metadata from the settings pane. Speaking of...
*At present, the settings pane contains a number of placeholder/in-production elements
Here's a brief overview of the various sub-sections in the settings pane, in order of appearance.
- Genome Arrangement - where you can change the genome spacing (vertical height) value of each genome group, as well as arrange groups by user-supplied ordering methods. Gene-cluster functionality is a work in progress :)
- Search - a versatile query tool
- Genomes - mostly placeholder data here, although genomes can be clicked-and-dragged to rearrange them in the visualization
- Group Layers - rearrange the constituent layers for each group. Show/hide layers, and recolor additional data layers
- Scale - change values for the ruler layer in each genome group
- Bookmarks - bookmarks are metadata at the sequence level. A bookmark saves the start/stop positions of your current zoom-level along with a title and description. Bookmarks will continue to be built out to persist additional session data.
- Gene Arrows/Links/Labels - all kinds of gene visualization stuff! too much to list!
- Pick any gene and choose an annotation item to query - then try querying from the settings pane
- Did the above query zoom to a specific section of the sequence? Try saving a bookmark that reflects your search criteria.
- Change the "Color genes by" value from default to
COG_CATEGORY- Check the "Link gene/label source" checkbox and select a new "Color genes by" value
- Batch color gene-arrows by any criteria you'd like. Does this work as expected?
- Reset function colors (bug* move the navbar to trigger a re-render)
- We can also edit cosmetics of multiple genes at once manually using the lasso menu
- Use the mouse drag box to select multiple genes from a single genome
- From this menu, batch color the selected genes and add a gene set label which will appear above the individual gene labels
- Now, make an additional selection that includes some of the genes you selected previously. You should notice that you are not able to create a set - label for these genes since they overlap with an existing label
- What worked as expected? what didn't?
- Was there any core functionality that you felt was lacking? missing entirely?