Graph interaction
There a handful of event interactions that are possible with the plasmid network in pATLAS.
At the bottom and center of the page there are 6 buttons, 4 enabled and 2 disabled by default.
The leftmost button with a play sign allow the force directed layout to start computing again. By default the force layout is paused in order to consume less resources, however for instance after filtering the current selection the user may feel the need to further render the graph (separate the plasmids from each other). This button will change the behavior after being clicked, and then if clicked again it will pause the force layout.
The second leftmost button allows the user to make area selections using shift key + left mouse dragging to select plasmid in a rectangular area. Releasing shift key or left mouse click will release the selection area and color the selected plasmids in orange. To disable this mode, click this button again and it will turn grey again and lock area selection.
Area selections made with this function can be made through the reset nodes button or by clicking in the shift key without selecting anything.
Multiple selections are allowed and can be used to drag multiple clusters to a user specified area. To do so, users can make multiple area selections by pressing the shift key without releasing and making several selections with mouse drag and click. Note: Do not release shift key between multiple selections! If you do so, selection is finished.
After multiple selections are made they can be dragged to a user specified area, by pressing x key, while still pressing shift key and moving the mouse around. While pressing x key and shift key when you move the mouse (without right or left click or otherwise you will drag the entire graph), the selected plasmids (in orange) will move to according to the mouse movement.
At the middle of these 6 buttons there are two buttons that control the zooming level, a zoom in button and a zoom out button.
Button that centers the graph on the node with more links currently displayed. This is particularly useful if you lost track of the cloud of plasmids.
The two arrow buttons on the rightmost side of these 6 buttons are disabled by default and they are only enabled when multiple JSON files are loaded through the import of mapping, mash screen or sequence results.
Nodes can be clicked and a popup will open with the metadata for that plasmid. See plasmid popup.