src/hg/makeDb/trackDb/README 1.83
1.83 2009/07/17 22:02:52 kuhn
a few typos
Index: src/hg/makeDb/trackDb/README
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/README,v
retrieving revision 1.82
retrieving revision 1.83
diff -b -B -U 4 -r1.82 -r1.83
--- src/hg/makeDb/trackDb/README 7 Jul 2009 01:07:13 -0000 1.82
+++ src/hg/makeDb/trackDb/README 17 Jul 2009 22:02:52 -0000 1.83
@@ -581,9 +581,9 @@
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 "demension" grid of subgroups.
+3) Matrix selection of subgroups. A 2 or 3 "dimension" grid of subgroups.
See MATRIX below.
4) Subgroup buttons. This happens if you have subgroups but no 'allButtonPair"
or "dimensions" defined.
@@ -632,15 +632,15 @@
"noInherit on" setting, and all the proper settings for the subtrack type.
MULTI-VIEW VISIBILITY DEFAULTS
------------------------------
- Since using multi-view represents two levels of drop-downs controlling whether a
- subtrack will be displayed, and since the "visibility' setting on the composite
+ Because using multi-view represents two levels of drop-downs controlling whether a
+ subtrack will be displayed, and because the "visibility' setting on the composite
(parent) track controls the default setting (eg 'dense'), it is necessary to
have an additional setting for the multi-view defaults:
visibilityViewDefaults HMM=pack WIN=pack+ SIG=full ALN=hide
By adding a '+' at the end of a default visibility, the view's configuration
- settings (if any) will be displayed be default.
+ settings (if any) will be displayed by default.
MULTI-VIEW INDIVIDUAL SUBTRACK CONFIGURATION
--------------------------------------------
While in many cases all subtracks for a given view type should share the same
@@ -659,9 +659,9 @@
The default settings for a view come from a random subtrack that belongs to that view
Since some defaults must be different for individual subtracks, the view's defaults
must be explicitly set. To do this use the following setting
settingsByView Signal:viewLimits=0:2,viewLimitsMax=0:40
- Here the view "Signal" is a wig wth data range of 0 to 40 and a default view range of
+ Here the view "Signal" is a wig with data range of 0 to 40 and a default view range of
0 to 2. Currently only two parameters are supported and these are both for wig:
viewLimits=lower:upper # default is from the type line limits
viewLimitsMax=lower:upper # The max range (type wig lower upper)
@@ -677,10 +677,10 @@
subGroup2 cellType Cell_Type ES=ES MEF=MEF NP=NP EShyb=ES-hybrid
subGroup3 factor Factor K04=H3K4me3 K09=H3K9me3 K20=H4K20me3 K27=H3K27me3 K36=H3K36me3
sortOrder cellType=+ factor=+ view=-
These settings result in an original order by cellType,factor,view, but view is
-in reverse order. NOTE: the value sorted will be the subGroup Ids, NOT the values.
-In the example, subGroup3 refers to factors with values displayed in the UI like
+in reverse order. [why reverse order??] NOTE: the value sorted will be the subGroup Ids, NOT the values.
+In the example, subGroup3 refers to factors with values displayed in the UI such as
"H4K20me3" and "H4K20me3". An alphabetic sort of these values would place H4K20me3
before H4K20me3. However the actual sort will be of the Ids K09 and K20, which will
result in a more desirable order. NOTE: At some time, sortOrder may be extended to
allow sorting by shortLabel and longLabel, but currently only subgroups are sortable.
@@ -727,15 +727,15 @@
Certain specific terms may carry special meanings in code:
(see controlledVvocabulary below)
dateSubmitted,dateUnrestricted used by ENCODE
fileName is converted into a link to the downloads directory in wgEncode
- dataVersion is show separately from metadata
+ dataVersion is shown separately from metadata
which is seen below.
CONTROLLED VOCABULARY
---------------------
-A special feature of the whole genome ENCODE consortium effort is that there
+A special feature of the whole-genome ENCODE consortium effort is that there
are standardized cellTypes, antibodies and other known entities that are
defined in a "controlled vocabulary". The definitions of the vocabulary will
be reachable from the hgTrackUi page but this special case must be defined in
the trackDb.ra file. To do this, use the controlledVocabulary setting. Its