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Map Viewer | Map Search | Feature Search | Matrix | Map Sets | Feature Types | Map Types | Species | Map Details | Feature Details | Feature Alias Details | Evidence Types | Correspondence Details | Imported Links
CMap Concepts
Maps and Map Sets
In CMap, a map is a linear array of interconnected
features. This could represent a single linkage group in the
case of a genetic map, or a single contig for physical maps.
Related maps are grouped into map sets. Generally, these
are the result of a particular study, such as the set of linkage
groups produced by a genetic mapping study. For more
information about the map sets contained in the database, visit
the Map Set Info page.
Reference and Comparative Maps
To set up a comparison, a user first selects a reference map
set, then a reference map. This serves as the basis for
any comparisons that the user chooses to make. Once the
reference map image has been rendered, the user is given the
option to select one or two comparative maps. These
comparative maps may be added to both the left and the right of
the reference map. The user may keep adding additional maps for
as long as valid comparisons are available.
Features and Feature Types
Any item that is positioned on a map is called a feature.
The position may be either a point or an interval. Different
feature types are represented by different shapes (such
as horizontal tick marks [for points], line intervals, boxes,
arrows, etc.) or different colors. For more information on any
feature, click on it to view the corresponding feature
detail page.
Correspondences
The lines that connect features on one map to features on
another map denote correspondences. These
correspondences are assigned either automatically (based on
feature name) or manually by the data curator to designate
features on different maps that are equivalent in some manner.
Different colors represent different correspondence
types.
Map Viewer Options
- Ref. Set
-
Select a reference map set from the drop-down list. For
descriptions of all the map sets, see the Map Set Info page. You must select a
reference map set before any of the other options become
available. Note that selecting a new reference map set will
reset all other map options.
- Ref. Map
-
Select a reference map from the drop-down list. The list is
limited to maps that are part of the selected map set. You
must first select a reference map set before this option
becomes available. Choosing a reference map allows other
options to become available.
- Start
-
Enter a position to begin drawing the map. By default, the
actual start position of the map is used. Use this in
conjuction with the "End" option below to zoom in to
a particular region of the map.
- End
-
Enter a position at which map drawing shall stop. By default,
is the actual end position of the map is used. Use this in
conjuction with the "Start" option above to zoom in
to a particular region of the map.
- Highlight
-
Enter features to highlight on the map. Separate multiple
features with commas or spaces. If you wish to highlight a feature
that has spaces in its name, then enclose the feature name in double
quotes.
- Comp. Map (Right)
-
Select a comparative map to add to the right of the map
display. Only maps which have some correspondence to the
rightmost map are listed. The number of correspondences is
shown in square brackets.
[See also "Comp. Map
(Left)".]
- Current Maps
-
From top to bottom, lists the names of the maps currently
being displayed from left to right. To remove a map
(including those exterior to it), click on "Delete".
The main reference map is denoted with "(Ref.)" and
cannot be deleted.
- Comp. Map (Left)
-
Select a comparative map to add to the left of the map
display. Only maps which have some correspondence to the
leftmost map are listed. The number of correspondences is
shown in square brackets.
[See also "Comp. Map
(Right)".]
- Image Size
-
Select the desired size of the image.
- Font Size
-
Select the desired size of the fonts.
- Image Type
-
Select the image format you prefer.
- Show Labels
-
Select which class of feature labels to show.
-
None: Show no labels.
-
Landmarks: Show labels of features designated as
landmarks or those with correspondences.
-
All: Show all labels that will fit in the image.
- Collapse Overlapping Features
-
Allows you to collapse spanning features of the same type which
occupy the exact same coordinates as other features.
- Min. No. Correspondences
-
Indicate an integer values of the minimum number of correspondences
that a map must have to another map in order to be displayed.
- Include Feature Types
-
Show only the selected feature types. Multiple types may be
selected (Ctrl-Click on most systems).
- Include Correspondence Types
-
Show only the selected correspondence types. Multiple types
may be selected (Ctrl-Click on most systems).
- Aggregate Correspondences
-
Draw all the correspondenses between each map as one line (the average
location on each map) or two lines (the span of locations on each map).
- Total Magnification
-
Draw the map taller by this multiple of magnification. This will affect
all the maps, including individually magnified maps.
- Draw Maps to Scale
-
Draw the maps that have the same base units to scale with respect to
each other. The base units must be defined as scalable in the config
file.
Map Image
Once a user has selected a reference map set and a reference
map, it is immediately rendered as a map image. By default, the
entire length of the map is displayed. At the top of the image
is a box in which is printed the species, map set name, and map
name as well as a combination of the following controls:
- i: View the info page for the map set
- ?: View the map details page for the map (for
"relational" maps, click directly on the map glyph
for this action)
- X: Delete the map from the viewer
- F: Flip the map
- M: View the Matrix for this map.
- N: Create a new map viewer with the map as the reference
A vertical scale bar indicates positions along the length of the
map. The distance measure (e.g., cM) being used is printed at
the bottom of the scale bar. Features are drawn at appropriate
positions. A legend for the various feature types shown on the
map is printed at the bottom of the image. Click on a feature
label to view the feature
details page for that feature.
Note that not every feature may be labeled. The drawing
algorithm will try to fit as many labels as it can, until there
is no more available space. To see more labels, you may wish to
increase the image size or decrease the font size. You may also
specify "Start" and "End" positions to zoom in to a particular
region on the reference map.
If two or more maps are being compared, each map will be drawn
in a separate regions. Adjacent maps will have correspondence
lines that connect corresponding features. The color of the
line depends on the type of correspondence, indicated in the
legend at the bottom of the map image.
In the lower-right-hand corner is a watermark indicating the version
of CMap used to draw the map. This is also hyperlinked to the CMap
homepage,
http://www.gmod.org/cmap.