Cytoscape_3/Cy3TestPlan/layout_menu

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a network file (eg. galFiltered.sif)
3. Click on Layout from the toolbar

L1

1. Click Rotate
2. Drag the pointer along the number line representing degree

The Tool Panel should appear at the bottom of the Control Panel with the Rotate tab selected. The graph should rotate through the number of degrees indicated (To hide the Tool Panel click Layout → Rotate again)

L2

1. Click Scale
2. Drag the pointer along the number line

The Tool Panel should appear at the bottom of the Control Panel with the Scale tab selected. The graph should change in size proportional to the number indicated. (To hide the Tool Panel click Layout → Scale again)

L3

1. Click Align and Distribute
2. Drag and select some nodes
3. Select some of the buttons from the Tool Panel

The Tool Panel should appear at the bottom of the Control Panel with the Align and Distribute tab selected. The buttons should arrange the nodes in various configurations. (To hide the Tool Panel click Layout → Align and Distribute again)

L4

To avoid repetition the Settings… sub menu contents will be tested under the JGraph and Cytoscape Layouts sub menus

L5

yFiles Layouts are tested under the core plugins test cases

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a network file (eg. galFiltered.gml)
3. Click on Layout from the toolbar

L7.1

Select Cytoscape Layouts → Inverted Self-Organising Map Layout

Nodes are clustered but not overlapping extensively. Edges are fairly long and angular with <90° angles

L7.2

Select Cytoscape Layouts → Edge-weighted Force directed (BioLayout) → (unweighted)

Edges are very long and nodes overlap. Network arranged in arrow or comet shape

L7.3

Select Cytoscape Layouts → Degree Sorted Circle Layout

The nodes of the main network are arranged at a locus equidistant from the centre of the circle and sorted numerically according to Degree starting at the bottom of the circle going clockwise

L7.4

Select Cytoscape Layouts → Grid Layout

The nodes should be arranged in an almost square grid

L7.5

Select Cytoscape Layouts → Attribute Circle Layout → Name

The nodes of the main network are arranged at a locus equidistant from the centre of the circle and sorted alphabetically according to Name starting at the bottom of the circle going anti-clockwise

L7.6

Select Cytoscape Layouts → Circular Layout → All Nodes

Some of the nodes from the main network form a circle with branches off it

L7.7

Select Cytoscape Layouts → Group Attributes Layout → All Nodes → Name

Nodes are arranged in a grid close to other nodes with similar Name distributed alphanumerically

L7.8

Select Prefuse Layouts → Force-Directed Layout → (unweighted)

Layout appears similar to Organic yFiles layout. Nodes and edges arranged to minimise force between them

L7.9

Select Cytoscape Layouts → Edge-weighted Spring Embedded → (unweighted)

Layout appears similar to Organic yFiles layout. Nodes and edges arranged to minimise force between them in an unweighted manner

L7.10

Select Cytoscape Layouts → Spring Embedded

Layout appears similar to Organic yFiles layout. Nodes and edges arranged to minimise force between them

L7.11

Select Cytoscape Layouts → Hierarchical → All Nodes

The graph should resemble a family tree, many of the edges have more than one angled bend

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a network file (eg. galFiltered.sif)

ML1

Select a node on the graph and drag it to a new position and then drop it

The node selected should be highlighted and the user should be able to move it around, the edges connected moving with it

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape 2. Import a network file (eg. galFiltered.sif)

AL1

The graph should take on one of the Cytoscape Automatic Layouts (in this case a grid)

Preconditions

Test Case ID

Instructions

Expected Results

Date Executed

Pass/Fail

1. Start Cytoscape
2. Import a network file (eg. galFiltered.sif)

YL1

Select Layout from the toolbar → yFiles → Circular

Graph should appear in a circular layout

YF2

Select Layout from the toolbar → yFiles → Organic

Graph should appear with highly connected nodes clustered and less connected nodes further away

YF3

Select Layout from the toolbar → yFiles → Hierarchic

Graph should resemble a family tree (especially apparent for hierarchic rankings

YF4

Select Layout from the toolbar → yFiles → Random

Graph should appear with random node placement

YF5

Select Layout from the toolbar → yFiles → Mirror X

Current graph should be an X-axis inversion of its previous layout

YF6

Select Layout from the toolbar → yFiles → Mirror Y

Current graph should be an Y-axis inversion of its previous layout

YF7

Select Layout from the toolbar → yFiles → Orthogonal

Nodes and edges should generate polygonal arrangements with right angles