# Cytoscape Formatting

## Manually format pathway maps for convenient viewing and proper node size

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 cyto_vis_auto and KEGG_lincs_auto from https://github.com/uc-bd2k/KEGGlincs/blob/master/R/cyto_vis_auto.R and https://github.com/uc-bd2k/KEGGlincs/blob/master/R/KEGG_lincs_auto.R.

### 2) ‘Re-lock’ the node width and height

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.

## Modify the threshold to label edges even if desired pathway has many edges

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.