Introduction to Maps
A guide through the basics of the SPARC Portal Maps interface
In this guide we will step you through the basics of the Maps interface:
Let’s start by looking at the controls available.
Controls
Figure 1: Maps interface controls
A. The dropdown in the top left corner displays the name of the currently viewed map/scaffold. If more than one view has been loaded then you can use the dropdown to change what is displayed. To find out more about working with different views see the “Working with multiple views in Maps” tutorial.
B. This dropdown allows you to change the Species on the default “MultiFlatmap.” When viewing other maps/scaffolds this dropdown will not appear.
C. The controls in this area allow you to choose what is displayed in the main view. Depending on the type of map/scaffold displayed this could be either Pathways or Regions. By using the tick boxes, parts of the map will be hidden allowing you to view other areas that may be obscured. If desired, this section can be collapsed using the chevron icon on the side. Also there is an option to change the background color to allow for easier viewing of maps and scaffolds that are in different colors.
D. There are four controls in the top right hand corner:
- Split Screen - Allows you to view maps and scaffolds next to each other. This button is only enabled when more than one map/scaffold has been loaded. To find out more about working with different views see the “Working with multiple views in Maps” tutorial.
- Help - Allows you to show all the tooltips relating to controls at the same time
- Full Screen - Allows you to toggle between a Full Screen view and a browser window view
- Permalink - Allows you to create a link that retains the state of your current working environment. This includes which maps/scaffolds are open and any display settings.
E. The overview panel shows you where in relation to the full view of the current map/scaffold. As you zoom in and out, a blue box will appear in the overview panel showing you how much of the map/scaffold is currently being displayed. NOTE: This control is not available on all maps/scaffolds.
F. The chevron on the right hand side of the screen allows the maps sidebar to be viewed. The sidebar allows you to find datasets, maps, and scaffolds. To find out more about working with the sidebar see the “How to use the sidebar in Maps” tutorial.
G. These controls allow you to control the zoom level of the map. You can zoom in and out and also select to fit all of the current map/scaffold into the current display window.
Figure 2: The display interface that allows manipulation of the flatmap visualisation
H. 3D map display. Clicking the Open 3D Map button prompts the multi-flatmap view with the 3D map. The 3D map can be closed by clicking the Close 3D Map button.
Figure 3: The multi-flatmap view with the 3D rat map displayed below.
Note:
Both flatmaps can be manipulated at the same time, including selection of organs. This can be changed with the toggle on the top of the flatmap, switching between Linked and Independent.
Figure 4: Toggle at the top of the flatmap to switch between linking the two maps together, or independent manipulation of each map. Hover over the question mark for more information.
I. Flatmap controls and help
- Split Screen - Clicking this button allows the user to view multiple maps/scaffolds at once. The multi-flatmap view can also be configured here. For more information refer to the Working with Multiple Views in Maps documentation.
Figure 5: Split screen toggle and options.
- Help - Clicking this button prompts support boxes throughout the map/scaffold display to provide further information on the features.
- Fullscreen - Clicking this button allows a fullscreen display of the map/scaffold.
- Permalink - Clicking this button generates a permalink to the current version and orientation of the map/scaffold display.
Figure 6: The generated permalink to the current version and orientation of the map/scaffold display.
J. The overview panel. The current location of the user in respect to the full view of the flatmap can be seen here. As the map is manipulated, a blue box indicates what region of the flatmap is being viewed.
K. The map sidebar. The arrow on the right hand side of the map interface opens the sidebar. Here datasets, maps, and scaffolds can be accessed. For more information refer to the How to use the sidebar in maps documentation.
Figure 7: The map sidebar. Datasets, scaffolds and more can be accessed here. Clicking on features in the flatmap prompts the sidebar with related information.
L. Zoom controls of the interface. The zoom level of the map/scaffold being currently viewed can be manipulated with these controls. The right-most button allows a fit-to-window display. Note that zooming in/out can also be achieved by scrolling.
Interacting with the display
The map/scaffold interface can be manipulated in various ways.
- When viewing the 2D flatmaps, left-clicking allows movement around the display.
- When viewing the 3D maps/scaffolds, left-clicking rotates the map/scaffold being viewed. Movement around the display can be achieved by right-clicking.
- Zooming in and out of the display can be achieved by scrolling, pitching in/out on a mousepad, or by the controls in the bottom left corner (as mentioned in part L of the Controls section).
Viewing anatomical features
Figure 8: Selecting an anatomical structure (e.g. the Liver) on the rat flatmap.
Hovering over anatomical features will highlight it and prompt a tooltip with the feature ID. Clicking on these features will highlight it in green and outline it in red. Clicking the teardrop map marker will prompt the flatmap sidebar and provide all datasets and/or scaffolds relating to the selected feature. As seen in Figure 8, the liver has been selected and highlighted. Clicking the teardrop map marker prompts the flatmap sidebar with datasets relating to the liver. For more information, refer to the How to use the sidebar in Maps documentation.
Viewing neuron pathways
In a similar manner, information on the neural pathways and other anatomical features can be observed. As seen in Figure 9, selecting the ‘Neruon type sdcol g’ pathway prompts a tooltip that provides more information. Scrolling down in the tooltip reveals a Search for data on components button, shown in Figure 10. This prompts related datasets in the flatmap sidebar.
Figure 9: Selecting the pelvic ganglion highlights the feature and connected paths. Selecting the path ‘Neuron type sdcol g’ prompts a tooltip with further information.
Figure 10: Scrolling down the tooltip that appears when selecting neuron pathways, a ‘Search for data on components’ button appears.
Viewing scaffolds
Figure 11: Clicking on anatomical features like the urinary bladder opens the scaffold of the organ. Note that the multi-map view will not be triggered. The multi-view was set up for explanatory purposes.
Scaffolds can be viewed by clicking on the relevant anatomical features, like the urinary bladder. This will change the maps interface to the ‘Bladder Scaffold 3D’ view. Note that by utilising the multi-map view feature, both the flatmap and the scaffold can be visualised.
Updated 6 months ago