Advanced_Network_Merge_and_ID_Mapping/Merge_Manual

(Under construction)

Simple mode

1. Select a set operation (union, intersection and difference).
2. Select networks to be merged.
   • Note: for difference operation, only two networks are allowed and resulting network would be the first network except the common nodes and edges with the second one.

3. Click Merge to merge the selected networks based on node IDs.

   • . Note: ID based network merge will be not be supported in Cytoscape 3, and thus this simple mode will be removed then.

Advanced mode

1. Select a set operation.
2. Select networks to be merged.

3. Click Advanced Network Merge to merge networks based on node attributes.

4. Select an matching attribute for each network.
   • Matching attributes are used to match nodes among networks. If taking union, matched nodes will be merged into one in the resulting network.

   • Matching nodes in the same network is enabled as default, and thus nodes in the same network may be matched and merged into one in the resulting network. (To turn off matching nodes in the same network, select in the Advanced Option.)

   • ID mappings can be utilized for matching nodes (see the session of Using ID Mapping).

   • Note: this plugin assumes that each network has an node attribute of canonicalName and the values of this attribute are the same as the node ID. When choosing node ID as the matching attribute, canonicalName will be used instead. (This is for easy upgrading to Cytoscape 3.)

5. Specify how to merge the node/edge attributes in the merging networks into the attribute in the resulting network.
   • The columns except the last two are corresponding to the selected merging networks; The second last column is for the merged networks; And the last column is for specify the attribute types for new attributes.
   • Attributes from different merging networks in a row will be merged into one in the resulting network.
   • By default, ID and canonicalName the matching attributes will be merged separately (the first three row). The name of the attribute merged from matching attributes can be changed by double click (only new names are allowed).
   • If ID mappings have been imported, the matching attributes will be mapped to the destination ID types and then merged.
   • By default, the canonicalName attributes from each merging network will be backed up as the last several rows.
   • Attributes with the same name in the merging networks can be merged into the attribute with that same name in the resulting network.
   • Attributes with different name in the merging networks can only be merged into a new attribute (different name from the existing attribute names) in the resulting network.
   • The attribute type of new attributes can be changed in the last column.
   • An attribute in the merged network is not necessarily merged from all merging networks, i.e., in the table, it is not necessary to specify each column for a row.

   • Select [DELETE THIS] at the end of each combobox will remove any attribute of the corresponding merging network from be merged into the corresponding attribute in the merged network.

   • If all the attributes of the merging networks in a row are 'deleted', that row will be deleted also.
   • Specify new merging attributes in the last row.

   • Click the name of the resulting network (Merged.Network by default) to change the network name.

6. Click Merge to merge the selected networks.

Using ID Mapping for Advanced Network Merge

1. ID mappings can be utilized for matching nodes.

2. Click Import ID mapping.

3. ID mapping from local and remote files are supported for the current version. (ID mapping from webservices and databases will be supported in future versions.)
4. Select ID mapping files.
   • A ID mapping file should be a tab-delimited text table file or MS Excel file (ref: import network from table).
     • Each column for one ID type.
     • Each row except the first one represents IDs of different types mapping to each other.
     • First row contains ID types.
     • Multiple IDs are allowed to be contained in one cell (One to many mapping, or IDs of the same type maps to each other). Use special comma to separate IDs.
5. Specify ID type(s) for each attribute.
   • Multiple ID types can be specified for one attribute.
   • ID mapping from multiple files can be added by select different files and add ID mapping for multiple times.
6. Select the destination ID type.
   • Selected attributes will be mapped to the destination ID type and stored in the merged attribute in the resulting network.

7. After all ID mapping added, click Preview to view all ID mappings and click OK to return all of these ID mappings for matching nodes.