0.9-1
* bug-fix: when flip=TRUE and SNP.name not null, the gene map was being
plotted over the heatmap. Thanks to Martin, Chia-Hsin Liu for reporting
the bug

0.9
* Renumber version to prepare for release of a version 1.0

0.3
* Added arguments 'flip', 'text' to LDheatmap().
* Added functions LDheatmap.plotGenes, plotGenes, LDheatmap.recombRate, 
  recombRate, LDheatmap.addAssociation.
* Added internal functions constructVP, drawLDheatmapGrob, moveTitles.

0.2-9
* data/datalist: Took care of the warning message related to undocumented data sets

0.2-8
* Missing links in LDheatmap.Rd were taken care of.
* Replace grid.prompt() with devAskNewPage() to fix the Warning Message 
given when the 'demo' is running.
 
0.2-7
* Change lower.tri(draw=T) to lower.tri(draw=TRUE) in LDheatmap.R.
* Replace the deprecated grid.prompt() function with devAskNewPage() for 
the Example in the LDheatmap fumction documentation (LDheatmap.Rd).

0.2-6
* Added "See LDheatmap vignette for details." to the Details section.

0.2-5
* 'datalist': "CEUData" and "CHBJPTData" added to fix the 
Warning Message.
  
0.2-4
* Added CITATION file to give information to the users how to cite the 
  LDheatmap Code Snippet.
* LDheatmap.Rd: added ``references" section. 
* LDheatmap(): removed `recording' argument from the functions: 
preDrawDetails.ldheatmap(), postDrawDetails.ldheatmap(), 
preDrawDetails.symbols() and  postDrawDetails.symbols().

0.2-3

demo(LDheatmap)
Revise the examples so that they correspond to the ones in the 
documentation of LDheatmap() function.

0.2-2

LDheatmap(): 
* Added argument 'pop' to control whether or not the heatmap viewport 
  is popped after drawing. The default is FALSE.
* Added argument 'vp.name' specifying the name of heatmap viewport.
* Now when SNP.name is provided and add.map=FALSE, the genetic map is not
  drawn but the SNP names provided are marked on the heatmap plot.
* Added argument 'add.key' to allow user to switch off the color legend.
* Default 'color' changed from 'heat.colors(20)' to 'grey.colors(2)'.

LDheatmap.marks() and LDheatmap.highlight():
* These functions now attempt detection of the viewport in which the target 
  heat map was drawn and navigate to it automatically. 

Data sets:
* Added example data-set: "CHBJPTData" containing "CHBJPTSNP" and "CHBJPTDist".
* Changed supplied data files names from 'LDheatmapData', 'HapMap.dat' and
  'distance' to 'CEUData', 'CEUSNP' and 'CEUDist' respectively.

Other:
* Removed 'myRainbow.colors()'
* Added internal functions preDrawDetails.ldheatmap, postDrawDetails.ldheatmap,
  preDrawDetails.symbols and postDrawDetails.symbols to enable resizing of 
  text when user resizes the window after drawing the heatmap.
* Simplified example of drawing two heat maps on same graphic device.

0.2-1
 
* Fixed bug of defaulting to black grid lines in new R version 2.3.0

0.2

Re-write of the function to make use of grid graphics. 
Grid graphics allows users to modify the heatmap and extend the function in
ways that are not possible with traditional R graphics. For examples of how
to modify the plot using tools from the grid package, see the examples in 
the LDheatmap help file.

Changes to function arguments:
1. The function now allows gdat to be one of the following: 
- a data frame of genotypes
- an object of class LDheatmap
- a matrix of pairwise LD measurements.
The purpose of allowing gdat to be an object of class LDheatmap is to 
enable recycling of the LD measures calculations, that can be time consuming for large data files, from previous calls.
If gdat is of class LDheatmap, the function recycles pairwise LD 
measurements from the original call and ignores the argument LDmeasure specified by the user in the second call.

2. Arguments x.image.show, y.image.show no longer used.
to control the size of the image, use the viewport command from the grid package.
See the LDheatmap help file for examples.

3. Changes to argument names: LDmeas is now LDmeasure, line.position is now
geneMapLocation, x.length.position is now geneMapLabelX and
y.length.position is now geneMapLabelY.

4. New argument newpage controls whether the heatmap is to be drawn on a
new page. Default is to draw on a new page.

5. New argument name specifies the name of the top-level grid graphical object (grob) created by a call to the function LDheatmap. 
See the examples for usage in the LDheatmap help file.

Changes to function output:
A list of class 'LDheatmap' is produced. The list consists of the following items:
LDmatrix - A matrix of linkage disequilibrium measurements.
LDheatmapGrob - A graphical object. This object is first drawn and than 
returned by the LDheatmap function.
heatmapVP - The Viewport in which the LDheatmap plot is drawn.
genetic.distances - Vector of physical or genetic map distances.

The LDheatmap plot output has been converted to grid graphics and is
comprised of the following editable grid objects (grobs):
"heatMap" - the color image of the heat map with its main title 
"geneMap" - the genetic map drawn on a diagonal line against the heatmap
"Key" - the color key legend
For further information on how to customise these objects, see
the package demo and the examples in the LDheatmap help file.

New functions:
1. LDheatmap.highlight - Highlight a genetic region in the LD heatmap.
2. LDheatmap.marks - Plot a symbol in the centers of cells 
representing the pairwise linkage disequilibria of specified pairs 
of SNPs.


0.1-5

 * Changed title in DESCRIPTION file

0.1-3

 * Enable user to select his own color scheme or blueToRed color scheme

0.1-2

 * Fixed bug in number calculated for legend "Genetic Map Length:"

0.1-1

 * Changed DESCRIPTION file
