50879a38007a5d65c7212f08a4050b36addee76a
jcasper
Mon Apr 15 16:04:43 2019 -0700
Cleaning up a few HTML tags while trying to track down bug, refs #23323
diff --git src/hg/htdocs/inc/hgCollectionHelpInclude.html src/hg/htdocs/inc/hgCollectionHelpInclude.html
index cbce744..eb9ebb1 100755
--- src/hg/htdocs/inc/hgCollectionHelpInclude.html
+++ src/hg/htdocs/inc/hgCollectionHelpInclude.html
@@ -1,289 +1,289 @@
The Track Collection Builder (My Data > Track Collection
Builder) is a tool that allows multiple tracks to be copied and grouped together into one composite
-track or "collection." A
+track or "collection." A
composite
track can be thought of as a container for grouping a set of similar-type annotation tracks.
Quick video demo
Two-minute video demo of Track Collection Builder:
Supported Data Types
Only the following continuous-value graphing track types can be added to a collection:
The "Collected Tracks" top right pane displays all created collections.
Click the button to make a new collection.
On creation, enter a name, description and optional graph color in the pop-up box.
Once saved, double-click a collection's folder icon to edit the name, description, and
subtrack colors.
See 'Step 2' below to add/remove tracks.
To remove a collection: select it, right-click (or select multiple, 'command + click',
'shift + click') and click .
Collection changes are saved after going to the browser window. To remove changes since the
last save, click (upper right).
Click (upper right) to see collections
in the browser.
From the browser, right-click to configure the collection (see 'Step 3' below).
Step 2: Add tracks to a collection
The 'Available Tracks' top left pane displays all available graphing tracks that can be added to
any collection.
Available Tracks (left window pane)
Click the small arrow to the left of folder icons to expand/contract tracks.
'Visible Tracks' folder: Lists tracks that are visible (not set to 'hide') in the browser.
Folders below 'Visible Tracks': Lists all available tracks, regardless of
visibility, by browser category.
Load external tracks: custom tracks & hub tracks
Load supported custom
tracks into the browser and select them from the 'Available Tracks' pane.
To add a track from a hub, load the hub first, and then select the track from 'Available
Tracks'. Collections must contain subtracks that all belong to the same assembly.
Add & remove tracks
To add a track to a collection, click the green "plus"
symbol to the
left of each track, or right-click (or select multiple, 'command + click', 'shift + click')
and .
To remove a track from a collection, click the red "minus"
symbol
to the left of each track, or right-click and .
A single track can be added/duplicated multiple times into a single collection.
A single track can be added to multiple collections, where various comparison views can be
applied (see 'Step 4' below).
Drag and drop to reorder tracks within a collection.
To add tracks directly from the browser, right click on the track to see options.
Step 3: Browser viewing options
When viewing collections within the browser, the following viewing options are
available:
Re-order collections within the browser
Drag and drop collections (composite tracks) within the browser to rearrange the order
in which they appear in the browser.
Sorting by similarity
To sort by similarity, right-click the collection in the browser window and select
. For the given region visible in the browser
window, tracks within the collection will sort in order of similarity. Sorting by similarity
counts the number of pixels set in each column and then uses matrices to build a neighbor
joined tree, which then has its leaves sorted to make an optimal ordering. The source of the
optimal leaf sorting algorithm is credited below.
Sorting by magnitude
To sort by magnitude, right-click the collection in the browser window and select
. For the given region visible in the browser
window, tracks within the collection will sort in order of magnitude, with the highest in
magnitude at the top of the subtracks in the collection where magnitude reflects the
total number of pixels set when drawing each track.
Tip: Displaying collection names in the browser:
-
+
Once a collection has been created and tracks have been added to it, click
(upper right) to view the collection in the
browser window. In the browser, mouse-over the gray vertical buttons at the left window frame to
- see the name of each collection.
+ see the name of each collection.
-
+
Step 4: Configure collection
Track Color:
Track color for all subtracks in a collection can be set by double-clicking the collection
folder in the right window of the Track Collection Builder, which will display a pop-up dialog
box. In the pop-up, a color can be set for the subtracks in the collection. Color will be
applied as a gradient to subtracks in the collection (e.g., if red is selected, the
subtrack graphs will appear in varied shades of red within the browser window).
To revert back to the original track color, change the color picker to '#000000'. To change the
track color to black rather than any non-black original color, set the color picker to any shade
of black besides '#000000', such as '#000001'. For example, if a track's original color is
green, you can change it to red with the color picker. To change this track back to the original
color (green), set the color picker to '#000000'. If you instead want to change that track to
black, select any shade of black in the color picker, such as '#000001'.
Default setting; no overlay/merge is applied. Subtracks appear as individual tracks
within the collection/composite.
Transparent
Subtrack graphs are merged together with transparent overlay views.
Solid
Subtrack graphs are merged together with solid overlay views.
Stacked
Subtrack graphs are layered horizontally with solid overlay views for each subtrack.
Add
Subtrack graphs are layered horizontally and merged into one solid overlay color; the
silhouette of 'stacked.' For this 'add' view, there is also the option to configure how
missing data are treated (see section below).
Subtract
The first (top) subtrack is subtracted from the sum of the others. Note: Re-order
collection subtracks in the 'Collected Tracks' pane to change which subtract is at the top.
For this 'subtract' view, there is also the option to configure how missing data are treated
(see section below).
-
+
Tracks in collections can be displayed with
multiWig aggregate/overlay "merge" methods (stacked, transparent, etc.) as well
- as new add & subtract options.
+ as new add & subtract options.
-
+
Missing data treatment:
Missing=0
Default setting. Missing data are replaced with a 0 (zero). Graphing will be drawn at the
zero point for the x-axis and y-axis (0,0).
- Note: Calculations (where 'Merge Method' = 'Add' or 'Subtract') will use a zero
+ Note: Calculations (where 'Merge Method' = 'Add' or 'Subtract') will use a zero
in the arithmetic.
Missing=missing
Graphing will not be drawn for missing data points. Where data are missing for any point
in the calculation, the calculated result for that position point will be missing.
Step 5: Saving and sharing collections
Collections will be available 48 hours before expiring. You must
save your session to
preserve collections long-term and to allow
sharing.
Even after saving collections and their configurations in a session, it is still highly recommended
to keep local back-ups of your session contents and any associated custom tracks.
