CMap User Tutorial

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CMap User Tutorial
CMap is a web-based application for viewing
genetic and comparative maps. It was originally
written for the Gramene project
(http//www.gramene.org/) and is now part of the
GMOD (Generic Model Organism Database) Project
(http//www.gmod.org/). This is a tutorial
created to help users understand how to use CMap
effectively.
Author Ken Y. Clark ltkclark_at_cshl.orggt
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CMap Menu
To navigate to the different functions of CMap,
you may use the CMap menu or follow links from
other pages. The currently active section will
be in bold and will not be hyperlinked (e.g.
Maps in the image below). Each section is
explained in this tutorial.
Home Page
Feature Type Info
Map Set Info
Map Viewer
Context-sensitive help
Map Type Info
Feature Search
Species Info
Evidence Type Info
Correspondence Matrix
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CMap Menu(Data Source Selector)
If more than one data source is available, the
data source select box will be visible. Choose
from the options and click the Data Source
button to change.
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Entering CMap

• There are three main entry points to viewing maps
  in CMap
• Comparative map viewer Choose a starting map
  and add comparative maps to the right or left
• Feature search Search for a particular feature
  by name or accession ID, species, and feature
  type
• Correspondence matrix View the number of
  correspondences among all maps and choose a pair
  to display in the viewer continue by adding
  more comparative maps

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Comparative Map Viewer(Initial View)
To access the map viewer, choose Maps from the
CMap menu.
Choose All or one species to display in Ref.
Set.
Quick start instructions
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Comparative Map Viewer(Species Selected)
Species limited to Rice
Only rice map sets appear, grouped by map types.
Select a map set and click Submit.
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Comparative Map Viewer(Map Set Selected)
Now choose a map and hit Submit
Click for Map Set Info
Click for Species Info
Click for Map Type Info
Map set info appears when map set is selected
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Comparative Map Viewer(Map Selected)
Start end points for reference map
Highlight features on map
Position other maps to the right or left
Drawing options
Restrict correspondences by evidence type
Hit Show Map button to submit choices
Highlight using either the features name, an
alias, or the features accession ID.
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Comparative Map Selection
You may place maps for comparison on the left and
right of the reference map (and continuing on, ad
infinitum).
Where to place the map(s)
Map type
The number in square brackets indicates
correspondences to the reference map
Choose one or all of the maps from this set
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Drawing Options
Determines the vertical height of the image
Size of the font
Output type of image
Which feature labels to show
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Drawing Options
This options determines whether to use one glyph
for features that span a distance when they have
the same coordinates or to repeat the glyph for
each feature.
Not collapsed
Collapsed
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Drawing Options
Use a positive integer to determine the minimum
number of correspondences required from map to
map (especially helpful to filter out maps like
FPC contigs with just one or two correspondences
to the reference map). A later slide illustrates
this point.
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Drawing Options
Determines which feature types to include on the
maps. If no selection is made, all feature types
are included.
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Reference Map Image
Menu
Reference map (showing no feature labels)
Map legend
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Map Image
Here is the same map now showing all feature
labels.
Glyphs showing feature locations
Feature labels in same color as glyph
Map coordinate
Map units
all meaning all that will fit
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Map Menu
Species name
Map set name
Map name
Click for Map Set Info
Click for Map Details
Click to Flip map
Click to make a new view with this map
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Map Legend
Listing of all the feature types found on the
maps with their glyphs
Description of menu buttons
Hyperlink to GMOD/CMap homepage
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Adding Comparative Maps
Here the reference map (Rice-JRGP-1) is in the
middle and a QTL map has been placed to the left
and a genetic map to the right.
Features with correspondences appear in red
(noted in legend)
Lines show correspondences colors denote
evidence type (when multiple evidences support a
correspondence, the one with the highest rank is
used to color the line)
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Choosing Landmarks for Show Labels shows only
features tagged as landmarks and features with
correspondences, reducing the clutter of extra
labels.
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Comparative Maps
When comparative maps are added, the legend
expands to explain the colors of the
correspondence lines.
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Relational Maps
Some maps are considered relational maps
because they can only be drawn in relation to
some other map. FPC contigs such as those shown
here are an example. Their length is determined
by the distance covered by the corresponding
features on the reference map.
This contig is longer because the correspondences
to the reference map cover a wide area.
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Relational Maps
The selection of which relational maps is
automatic (as opposed to other maps where you can
select individual maps as you please). All the
maps which have correspondences to the reference
map are selected automatically. You can use the
Min. No. Correspondences to filter out the maps
with fewer than a specified number of
correspondences. Here is the same map comparison
requiring a minimum of 2 correspondences from any
map (contig) to the reference map.
To see the details of a relational map, click on
the map itself.
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Map Details
The map details page shows a comparison of
whatever map you clicked on with whatever maps
were on the right and left of the map. The map
you clicked on for the details is here considered
to be the reference map. You can control the
display of the maps on this form with the same
controls available on the main map viewer.
For relational maps, you click on the map
itself otherwise, click on the ? button above
the map.
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Map Details
Below the comparative map image you will find a
table containing details of every feature on the
reference map, including the features name,
type, position, and all its correspondences. The
View Feature Details Table link just below the
reference maps name at the top of the page will
take you to this table as shown here.
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Map Details
You can restrict the correspondence information
in the table to a particular map or map set.
Choose a map or map set from the select box
entitled Restrict by Map at the top of the table
Then click Submit
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Map Details
Click the Download Feature Data link to get all
the data in the table in a tab-delimited format.
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Data Navigation
Change page
Previous page
Current subset
Current page
Total number of records
Next page
Total number of pages
Every place where multiple records are returned
(as on the map details page), a consistent data
navigation bar is presented. If the number of
records returned is below a certain threshold
(usually 25), then all the data is shown. When
more than this is returned by a query, the items
are broken into pages which you can navigate with
this control. The current subset (26 to 50) of
the total (145) is shown along with the page
number (2) of the total number of pages of data
(6). When appropriate, links for the
Previous and Next pages will appear. Click
on these to move one page forward or backward, or
indicate the page you wish to see and click the
Page button.
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Map Details Feature Table
Click View Maps to see the reference map and
this comparative map in the viewer with the
correspondence highlighted.
Reference map name
Click feature name for the Feature Details page.
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Feature Search
To search for a feature, click on the Search
link in the CMap menu.
Choose a species
Choose a feature type
Search either the features name (and aliases) or
accession ID
Follow these tips for searching.
Indicate the feature name(s) you wish to search
for
optional
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Feature Search Results
Found 7,498 features with a name or alias
matching rm
Click here to view the Feature Details for this
feature
Click headers to sort data by the column.
Click on map set name to view Map Set Info page
Click here to view this feature highlighted on
this map
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Feature Details
To view the Feature Details page, click on the
name of a feature on a map or in the Search
results. This page displays a features
accession ID, type, name, any aliases, its map
and location as well as any applicable attributes
or cross-references assigned by the curator. In
addition, all the correspondences are displayed
in a table.
Follow links to detail pages.
Click an evidence type to view the Evidence Type
Info page.
Show Maps will display a comparison of the map
above to this map with the two features
highlighted.
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Correspondence Matrix
The matrix is a cross-tabulated table showing the
number of correspondences among all the map sets.
When you first visit the matrix, you will be
prompted to restrict the reference maps (the
rows) by map type and/or species as the table can
be quite large.
To view the correspondence matrix, click on the
Matrix link in the CMap menu.
Choose a map type and/or species
Click Submit
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Correspondence Matrix
After optionally choosing a map type and/or
species, the matrix will display all the
correspondences from all the map sets which can
act as reference maps to all the other map sets
in CMap.
Matrix restricted to Barley map sets
Click on a map set name to restrict to just the
maps in that set (see next slide).
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Correspondence Matrix
Here the reference set column has been limited to
just one set (see previous slide).
When only one reference set is displayed, the
individual maps are display. Clicking on a
number in the cell will take you to the viewer
showing the comparison of the map to all the maps
of the comparative set.
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Correspondence Matrix
When multiple reference sets are displayed,
clicking on a number in this view will restrict
the matrix to just the maps in these two map sets
(see next slide).
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Correspondence Matrix
Here both the reference and comparative sets have
been limited to just one set showing map-to-map
correspondences.
When both the reference and comparative maps sets
are limited to one, clicking on a number in the
matrix will take you to the viewer showing a
comparison of just two maps from each set.
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Correspondence Matrix
When the reference set is limited to just one set
and the comparative maps (the top row) is
restricted to one relational map set, the number
of correspondences from the individual reference
maps to all the maps of the comparative set are
shown (i.e. the individual maps of the
comparative set are not shown).
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Correspondence Matrix
Clicking on a comparative map set in the top row
will restrict the top row to just that set (see
next slide).
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Correspondence Matrix
Here the comparative maps (in the top row) have
been limited to just one map set.
Clicking the number in this view will
additionally break down the matrix map-by-map.
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Map Set Info
This page contains information on all the map
sets, including their species, map type, names
(short and long), any additional attributes
the curator has assigned (e.g., Description),
the names of the maps in the set (for
non-relational maps) with links to view those
maps (or all) in the viewer, and the feature
types occuring on the maps in the set. There can
be many map sets on the page, so you can restrict
the sets with the controls at the top of the page.
To view the Map Set Info page, click on the
Map Sets link in the CMap menu.
Choose a species and/or a map type to restrict
the map sets by and hit Submit.
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Map Set Info
A link to the map set in the viewer
A link to the Species Info page for this species
A link to view the map(s) in the viewer
A link to view the Feature Type Info page for
each feature type in this map set
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Feature Type Info
To view the Feature Type Info page, click on
the Feature Types link in the CMap menu.
This page shows all the feature types used to
classify the map features in CMap. Each feature
type has a name, a color and a shape. The
curator may additionally assign other attributes
(such as a Description) and cross-references.
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Map Type Info
To view the Map Type Info page, click on the
Map Types link in the CMap menu.
This page displays all the map types used to
classify the maps in CMap. Each map type has a
name, an accession ID, the map units used for
maps of this type (e.g. bp for base pair or
cM for centimorgans), an indication as to
whether maps of this type are relational, and
an indication of how maps of this are normally
drawn (though this can be overridden at the map
set level).
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Correspondence Evidence Info
To view the Correspondence Evidence page, click
on the Evidence Types link in the CMap menu.
This page contains the name of each evidence type
used to support the correspondences in CMap.
Each evidence has an accession ID, a rank
relative to the other evidence types, and an
assigned color for the line drawn on the map to
differentiate the correspondence.
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Species Info
To view the Species Info table, click on the
Species link in the CMap menu.
This page contains the species common and full
names along with any other attributes and
cross-references the curators have created.
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Help
To view the context-sensitive help, click on the
Help link in the CMap menu.
Current help section in bold
Use the help sub-menu to view other help sections.
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End
This completes the CMap user tutorial. If you
have further questions, please feel free to write
the CMap development list at gmod-cmap_at_lists.sourc
eforge.net.