r-cran-gplots 2.11.3-1 / usr / lib / R / site-library / gplots / NEWS

Release 2.11.3 - 2013-06-27
---------------------------

Enhancements:

- Modify sinkplot() to use a local environment rather than the global
  environment, to conform to CRAN policies.

Bug Fixes:

- Fixed typo/spelling error in plotmeans() man page.

Other changes


Release 2.11.2 - 2013-03-24
---------------------------

Enhancements:

- Add ci.width argument to barplot2() to allow varying the length of
  the 't' at the end of confidence interval bars.

Bug Fixes:

- Fix error in heatmap.2 when colsep argument had length 1.

Updates:

- Update manual page for lowess.default() to
  match changed argument list for lowess() in R 3.0.0


Release 2.11.1 - 2012-12-14
---------------------------

Bug Fixes:

- Replace corrupted BalloonPlot.pdf in inst/doc.


Release 2.11.0 - 2012-06-08
---------------------------

New Features:

- Objects returned by hist2d() have been changed:
  1) $x and $y now contain the n midpoints of the bins in each direction
  2) $x.breaks, $y.breaks now contain the n+1 limits of the bins in
  each direction.

- Add lwd argument to plotmeans().

Bug Fixes:

- Correct error in handling binning in hist2d(): (N+1)x(N+1) bins were
   being created instead of NxN bins, and the highest row/column in
   each direction was being omitted from the results and plot.

- Changes to fix R CMD check warnings


Release 2.10.1 - 2011-09-02
---------------------------

New features:

- Make results of hist2d() and ci2d() into objects, and add print()
  methods to display them.

Release 2.10.0 - 2011-08-26
---------------------------

New Features:

- New ci2d() function to create 2-dimensional empirical confidence
  intervals utilizing KernSmooth:bkde2D and gplots::hist2d().
  See ?ci2d for details.

- Add 'alpha' argument to rich.colors() to control transparency.

Improvements:

- Accellerate hist2d by replacing for() loop with tapply(), and allow
  user to specify summary function applied (per suggestion by Peter
  Hagedorn).

Bug Fixes:

- Correct error in heatmap.2() that arises when data includes NA values
  (identified by Melissa Key).


Release 2.8.0 - 2010-06-10
--------------------------

Improvements:

- venn() now returns an object of class venn() and a plot method for
  this class is provided.

- Manual page for venn has been improved, based on contributions by
  Steffen Moeller


Release 2.7.5 - ??
--------------------------

Improvements:

- Performance of 'hist2d' improved thanks to a suggestion from
  Joerg van den Hoff.

Release 2.7.4 - 2009-11-12
--------------------------

Bug Fixes:

- Correct bug reported by Alan Yong:  plotmeans() failed when bars=FALSE.

Release 2.7.3 - 2009-10-22
--------------------------

Bug Fixes:

- Correct bug reported by Rudolf Talens: heatmap.2() incorrectly
  transposed the displayed matrix when the option symm=TRUE.


Release 2.7.2 - 2009-05-08
--------------------------

Bug Fixes:

- Correct bug reported by Ken Lo:  cox2hex() had blue and green
  components swapped.


Release 2.7.1 - 2009-05-08
--------------------------

New Features:


- Enhancements to heatmap.2()

    - New arguments 'lmat', 'lhei', and 'lwid' that allow controlling
      component plot layout.  Users can now resize and rearrange plot
      components.

    - heatmap.2() will now compute color breakpoints that are
      symmetric about 0 when the new 'symbreak' parameter is TRUE.  This
      parameter, as well as the symkey parameter now default to TRUE
      whenever negative values of x are present, and to FALSE othewise.

    - the heatmap.2() return value now includes additional useful
      information, including: call, rowMeans, rowSDs, colMeans,
      colSDs, carpet (reordered and scaled 'x' values), rowDendrogram,
      colDendrogram, breaks, col, vline, hline, and colorTable. Of
      these, the most useful are breaks, col, and colorTable.  The
      latter is a three-column data frame providing the lower and
      upper bound and color for each bin.

  See the manual page for complete details and examples.


- New function venn(), contributed by Steffen Moeller (Thanks
  Steffen!) to generate Venn diagrams for up to 5 sets. See ?venn for
  details.

- Performance of bandplot() has been dramatically improved, in part by
  using runsd() and runmean() from the caTools package.  As a
  consequence, gplots now depends on the caTools package.

- Improved performance of gplots::plot.lm for large lm objects by
  using the new bandplot() and by using fitted() instead of predict()
  to obtain y-hat.

- Add 'scale.range' argument to balloonplot(), option to scale
  balloons so [min,max]->[0,1] ('relative') or [0,max] -> [0,1]
  ('absolute').


Bug Fixes:

- balloonplot() now properly handles dimension labels provided by
  'xlab' and 'ylab'

- plotCI now properly handles 'NULL' and 'NA' values for ui, li, uiw,
  and liw.

- Corrections of minor typos in man pages

- Update Greg's email address to 'greg@random-technologies-llc.com'


Release 2.6.0 - 2008-04-07
--------------------------

New Features:

- heatmap() now allows control of the location of individual plot components
   (e.g. color key)

Bug Fixes:

- Fix bug in handling rowsep, per suggestion by Steven Paugh

- Fix examples for overplot()

- Two letter clarification of help text for heatmap.2()

- Restore plot layout settings to default state at end of ooplot() example

- Various typo fixes

Release 2.5.0 - 2007-11-02
--------------------------

New Features:

- textplot() now converts tab characters to spaces before processing to
  avoid problems with computing height and width of text that includes
  tabs.

- Add col2hex() function to convert color names to rgb hex codes

Bug Fixes:

- Correct balloonplot.default to properly show specified x and y axis
  labels when explicitly provided

- R/balloonplot.R: Correct error in balloonplot when z contains NA values.

- Fix typos and code/doc mismatches identified by the latest R CMD check

Other:

- Clarify GPL version

Release 2.4.0 - 2007-02-08
--------------------------

New Features:

- Add parameters to bandplot() to control line width and type.

- Add paramaeters to textplot.matrix() to allow specification of the
   color of the matrix data, rows, and column

Bug Fixes:


Other:


Release 2.3.2 - 2006-11-14
--------------------------

- heatmap.2.Rd: Fix example that was broken by changes in 2.3.0.


Release 2.3.1
-------------

- Changed maintainer back to Greg Warnes

- Updated Greg's email address

- heatmap.2.R: Fixed a bug which displayed warnings when Rowv and Colv
  were specified as dendrograms


Release 2.3.0
-------------

 - heatmap.2.R, heatmap.2.Rd:

          Updated the code and man page to make sure the Rowv and Colv
          values are properly handled

 - Added the tests directory



Release 2.2.0
-------------

 - plotmeans.R: Fixed bug in plotmeans - based on Stefano Calza's
	        suggestion (the function didn't account for factors
		unused levels, returning an error.)

 - exported plot.lm to NAMESPACE, Remove .Alias calls in plot.lm.R
 		since .Alias is defunct.

 - barplot2.R: Changed the default grey colors to heat colors, if
	       height is matrix

 - Updated Greg's email address

 - balloonplot.R: Recent changes to align row totals with the
	  	  overall total broke how the marginal cumulative
	  	  fractions were displayed. Added example using
	  	  Titanic data that exercises the multi-factor display.
 		  Added -.tex, .pdf files and figuers, and RNEWS article
		  in inst/doc

 - colorpanel.R: colorpanel now allows only 2 colors to be specified
		 if no 'middle' color is desired.


Release 2.0.8
-------------

 - Added DESCRIPTION and removed DESCRIPTION.in

 - Updated barplot2

 - Updated heatmap.2