Getting started
Launching it from a project
The Visualisation Designer runs as an application inside a Data Manager project, alongside your data rather than on your own machine.
- Open the project whose data you want to look at.
- Go to Run, find the DataVisualisation application, and start it. The launch dialog asks for a Viz application version — unless you have a reason to pin an older one, take the newest.
- When the instance is running, open it from Results.
The files the Data tab lists are the files in the project, and the visualisations you save are kept in the project’s database. You do not have to put a data file in the project first — the Data tab can also import one you upload from your computer or fetch from a URL, and that file is not added to the project (the dataset made from it is kept by the application).
An instance you stop using is eventually shut down by the Data Manager to free resources. That costs you nothing as long as you have saved: your visualisations live in the project, not in the instance. Launch it again and load them back.
The app bar
| Title | Your name, or the project — whatever the Data Manager told the instance about itself |
| Project | The Data Manager project the instance belongs to, if the Data Manager gave its name. A long name is cut short: point at it to see it in full. The browser tab is named after the project too |
| Name | The visualisation you are editing, in italics. Untitled until you have saved one |
| New | Start again with an empty canvas. If there are unsaved changes it asks first |
| Load | Open one of the visualisations saved in this project |
| Save | Write your changes back under the current name. Greyed out when there is nothing unsaved to write |
| Save as | Save under a new name, which then becomes the current one |
| ⚙ | Settings |
| ⛶ | Full screen, and back again |
Saving into the project
Save as asks for a name and saves the visualisation in the project’s database. Because it is in the project, everyone with access to the project can open it, and it is still there when you launch a new instance tomorrow. A name is kept exactly as you type it, spaces and punctuation included.
Save as never replaces another visualisation without asking: if the name is taken it says so, and offers Overwrite.
Load lists what is there. Each entry shows who first saved it and when, and who last saved it and when (the names are those of the people who launched the instance, so they are left out where there is none).
Click a name and then Load, or double-click it. The ✎ beside each entry renames it (to a name that is not already in use) and the 🗑 deletes it — deleting asks for confirmation, and cannot be undone.
When someone else has saved it first
If another browser, or another person, saves a visualisation while you have it open, your next save would replace their work. It does not: your changes stay exactly as they are on the canvas, Auto save pauses, and a message offers three choices:
- Reload (discard mine) opens what is saved now and drops your changes.
- Overwrite saves yours over theirs.
- Save as copy… keeps both, yours under a new name.
If the visualisation was deleted or renamed meanwhile, the choices are Save again and Save as copy….
Exporting and importing
The ⭳ beside an entry in Load downloads that visualisation as a
<name>.viz.json file, which you can keep, email, or put under version control.
Import in the same dialog adds the visualisations in one or more such files.
An import never replaces anything: if a name is taken it is added as
name (imported). It is also how you move a visualisation to another project;
the datasets it names must exist there too.
Loading a visualisation replaces what is currently on screen. Save first if you want to keep it.
Once a visualisation has a name, Auto save can save it after each change for you. It is one of the application settings.
Settings
The ⚙ in the app bar opens the application’s settings. It holds the Defaults that charts fall back on, the named Presets that charts share, and Auto save. These are stored in the project, so they are the same for everyone working in it. All of them, along with how each chart’s own settings work, are described under Settings.
Which files the application can see
The application lists the project directory recursively and offers everything it recognises:
| Kind | Extensions |
|---|---|
| Structures with data | .sdf, .sd |
| Tabular data | .csv, .tsv, .tab |
| SMILES lists | .smi, .txt |
| Protein structures | .pdb, .mmcif, .cif |
Compressed forms — .sdf.gz, .csv.gz and so on — are read directly, with no
need to unpack them first.
Files are read only when a node asks for one, so a project full of large files costs nothing until you pick one.