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3DScape User Manual

On startup, 3DScape is automaticlly bounded to the left panel of Cytoscape.

Follow these steps to begin visualization

You need to create/open a network in Cytoscape first, then follow "Step 1", select the network in 3DScape's droplist and press "Convert to 3D" button. After conversion, the network is layouted orderly. You can follow "Step 2" to apply a more meaningful layout, for large graphs this can take some time. If you have expression data to map to nodes, you need to load Expression Matrix from "Cytoscape file menu. After that you can follow "Step 3" to visualize expression data. There is also an slider for choosing which experiment in the Expression Matrix you want to show, and a play button for looping all experiments in the Expression Matrix.

Basic manipulations

Select

Left click node/edge will hightlight it, After selecting, coresponding description will be shown in the Node/Edge Attribute Viewer which is located in the bottom panel of Cytoscape. None of node shapes can be applied on selecting.

Zoom

Scroll the mouse wheel up to zoom in and down to zoom out.

Pan

Hold Alt key and right mouse button, drag mouse to move the scene.

Rotate

Hold right mouse button and drag mouse to rotate the scene.

Search

Input a label of node, 3DScape help you find the location of the node. The label is case insensitive, after input, press the button to the right. If a node with that label existed, it will be centered on the scene.

Customize network appearances

Node labels: Toggle whether or not show node labels for all graphs.

Node shape: Set shapes for all nodes, only None can be used when on selection.

Background: Set background color 1 and background color 2 for the foreground graph.

Color key: Set colors for expression data, left one for negative value, right one for positive value.

Distribution: Set how colors are distributed across negative value and positive value.

Apply colors: Set whether to apply expression color to Nodes/Edges, or both.

Edge width: Set the width for glowing effect when displaying expression data.