The following two steps must be followed to reproduce the pathway maps as seen
in the workflows for users without RCy3 available on their system. If RCy3 is
available, please use the functions
from https://github.com/uc-bd2k/KEGGlincs/blob/master/R/cyto_vis_auto.R and
Otherwise please follow the steps outlined below.
Neither this package's author nor other collaborators working on similar projects using Cytoscape via cyREST understand why this step is neccessary.
First, locate the 'Style' tab under the Control Panel
Then, scroll down [if needed] to the bottom of the window and locate the box labelled "Lock node width and height".
The box should be checked; uncheck the box, then re-check it - the nodes should then convert to their intended width/height format.
If a pathway has a large number of edges (for example the Fox0 pathway showcased in Workflow 1), users can adjust Cytoscape settings to render the edge labels by selecting following the path Edit > Preferences > Properties and selecting render.edgeLabelThreshold. Click 'Modify' and increase the value as desired [or until edge labels become visible]. The default setting in Cytoscape is 200.
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.