src/hg/makeDb/trackDb/README 1.90

Index: src/hg/makeDb/trackDb/README
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/README,v
retrieving revision 1.89
retrieving revision 1.90
diff -b -B -U 4 -r1.89 -r1.90
--- src/hg/makeDb/trackDb/README	1 Nov 2009 21:24:23 -0000	1.89
+++ src/hg/makeDb/trackDb/README	11 Nov 2009 22:25:31 -0000	1.90
@@ -605,9 +605,9 @@
 1) Select the check boxes for individual subtracks - no special settings needed
 2) Add All [+][-] buttons - To the composte track add the setting below.
    allButtonPair on
    Not compatible with either of the next two methods
-3) Matrix selection of subgroups.  A 2 or 3 "dimension" grid of subgroups.
+3) Matrix selection of subgroups.  A 2 "dimension" grid of subgroups.
    See MATRIX below.
 4) Subgroup buttons.  This happens if you have subgroups but no 'allButtonPair"
    or "dimensions" defined.
 
@@ -660,9 +660,21 @@
     dimensions dimensionX=cellType dimensionY=factor
 This will result in a composite track configuration page with a matrix of
 check boxes with 'Cell Types' along the X axis and 'Factors' along the Y.  All
 individual subtracks will be displayed below, but the matix of check boxes will
-allow easy selection by subgrouping.
+allow easy selection by subgrouping.  The dimensions X&Y have no explicit defaults
+(checked or unchecked) declared.  This is becuase their state can be determined by
+default settings of the tracks that belong to them.
+
+NOTE: Additional dimensions 'A'-'W' and 'Z' (called 'ABC' dimensions) may be added.
+However any 'ABC' dimensions will not be part of the matrix, but appear above it as
+single rows of checkboxes.  Unlike X&Y, any 'ABC' dimensions must have explicit
+defaults set with the following:
+    dimensions dimensionX=cellType dimensionY=factor dimA=rep dimB=prot
+    dimensionAchecked rep1
+    dimensionBchecked protA,protB
+This setting says that replicate 1 and protocols A and B are checked by default but
+all other replicates and protocols are unchecked by default.
 
 VIEWS or MULTI-VIEW
 -------------------
 A composite track may have subtracks with similar data subtracks which have
@@ -803,8 +815,13 @@
 term "estro-134/Pro-93a" in the controlled vocabulary file.  A more complete definition
 of what that term means, including a protocol, may be provided when the controlled
 vocab term is looked up and presented to the user.
 
+A special trick can be included in the label.  In the example label if
+"Estrogen_and_Progesterone" were replaced with "Estrogen and_Progesterone", then
+only the first part of the label (Estrogen) would be represented as a link to the controlled
+vocabulary.
+
 EXAMPLE of Composite Track with ADDITIONAL OPTIONS
 -------------------------------------------------
 track broadChromatinChIPSeq
 compositeTrack on