#acl All:read
= Master Maps - an implementation by Oliver =

== Example: ==
 * load the attached [[attachment:Master_Map_Oliver1.cys | session file ]]
 * ignore the Networks EM1 - EM3 and directly go to the "Master Map"
 * switch the visual Style between EM1, EM2, EM3 and Master

== How to manually create a Master Map: ==
 * create a couple of Enrichment Maps in one session
 * Merge Networks to a Master Map (Merge Networks Plugin - Union)
 * for each Enrichment Map:
   * create Node-Attribute (String) "is_significant_in_EM#" and default it to "false" (as a flag to see in which analysis the gene set came up)
   * set "is_significant_in_EM#" to "true" for all gene-sets in Enrichment Map EM# (that have non-empty attributes EM#_...)
 * for each Visual Style "EM#":
   * create discrete Mapping of "is_significant_in_EM#" to Node Opacity: true=255.0; false=100
   * create discrete Mapping of "is_significant_in_EM#" to Node Border Opacity: true=255.0; false=100

 * Master Map Style:
   * create Node Attribute "Master_formatted_Name" and copy each "EM#_formatted_Name" to this Attribute
   * create Node Attribute "Master_Colouring_dataset1" and copy each "EM#_Colouring_dataset1" to this Attribute
   * create Node Attribute "Master_gs_size_dataset1" and copy each "EM#_gs_size_dataset1" to this Attribute
   * create Node Attribute "Master_Genes" and copy each "EM#_Genes" to this Attribute
   * create Edge Attribute "Master_similarity_coeffecient" and copy each "EM#_similarity_coeffecient" to this Attribute
   * create Visual Style "Master Map" based on "EM#"
     * map Edge Line Width with "Master_similarity_coeffecient"
     * map Node Color with "Master_Colouring_dataset1"
     * map Node Label with "Master_formatted_Name"
     * map Node size with "Master_gs_size_dataset1"

== How to do it programmatically ==
 same as above plus:
 * re-calculate overlap to capture all gene-set combinations
 * calculate an overall colouring value (e.g. most extreme, average)
 * associate new instance of !EnrichmentMapParameters with the map, that we can use the slider-bars, too<<BR>>(and maybe also run the Signature Post-Analysis)
 * join expression data from EM# Maps and attach it to the Mastermap (we can eliminate identical columns to reduce the size)


== Example Maps: ==
 {{attachment:MasterMap_EM1_style.png|trunc Notch vs Ctrl|width=600}} {{attachment:MasterMap_EM2_style.png|absent Notch vs Ctrl|width=600}}<<BR>>
 {{attachment:MasterMap_EM3_style.png|wt Notch vs Ctrl|width=600}}    {{attachment:MasterMap_master_style.png|Master Map Style|width=600}}<<BR>>