/usr/lib/R/site-library/gplots/NEWS is in r-cran-gplots 3.0.1-2.1.
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--------------------------
Bug Fixes:
- An error in plotLowess() prevented it from finding objects in
the caller's environment.
- The manual page for heatmap.2() stated the incorrect type for
the 'layout' element of the return list. It is a named list,
not a named numeric vector.
Release 3.0.0 - 2016-03-28
---------------------------
New Features:
- venn():
- now support matrices of indicator values. Previously indicator
values were only supported when supplied as a dataframe.
- The 'intersections' attribute returned from venn() has been
improved so that goups are labeled using set names instead
of indicators, and are ordered from simplest to most complex
set intersection.
- New angleAxis() function to create axis labels with rotated text.
- heatmap.2():
- heatmap.2() can now be used to plot subsets of a previous
heatmap.
- Decrease the granularity of the carpet in heatmap.2()'s
color key to avoid visual artifacts.
- Returned object now includes 'layout' element that contains
layout information. (Patch provided by Jenny Drnevich.)
- lowess():
- New function plotLowess() to display a scatter plot with a
superimposed lowess curve.
- The lowess() functions now returns a list object of class
'lowess'
- A new lowess method for plot() method for 'lowess' objects
that generates a scatterplot of the raw data with a lowess
curve superimposed.
Bug Fixes:
- Defunct message for boxplot.n() was recommending the wrong
function.
- heatmap.2():
- Remove debugging print() statement.
- Now properly sets 'srtCol' default if missing and 'colCol' is
specified.
- Corrected a bug causing "Error in plot.new() : figure margins
too large" to occur when 'key=FALSE'. (Reported and patch
provided by Sveinung Gundersen.)
- Corrected a bug causing an error when "Rowv=FALSE" or "Colv=FALSE".
- Corrected message when "Rowv=FALSE" or "Colv=FALSE" and the the
"dendrogram" argument requested the corresponding dendrogram.
- venn():
- Fix warning message that was missing spaces between words.
Other Changes:
- The smartlegend(), plot.lm2(), and boxplot.n() functions are now
defunct. Please use grephics::legend(), lmplot2() or boxplot2()
respectively.
Release 2.17.0 - 2015-05-01
---------------------------
New Features:
- heatmap.2() has two new arguments, 'colRow' and 'colCol' to control
the color of row and column text labels. See the man page for
examples.
- heatmap.2() has been modified to make it easier to extract and plot
subclusters from a large heatmap. Simply pass the dendrogram of the
subcluster together with the full data matrix and, optionally, the
breaks of the full heatmap in order to obtain the same color
scaling. (Suggestion and patch contributed by Ilia Kats.)
- venn() now returns a list of the members of each set intersection in
the attribute 'intersections'. This can be disabled using the
argument 'intersection=FALSE' (Patch by Steffen Möller.)
Bug Fixes:
- In heatmap.2(), the color key now properly handles color breaks that
are not equally spaced. (Issue reported by Tim Richter-Heitmann.)
- In heatmap.2(), row/column traces in could be plotted on the wrong
row/column.
- plotCI() now properly respects the 'type=' argument. (Bug report
and correction by Wiktor Żelazny.)
- Remove stray browser() call from overplot()
- In the balloonplot() examples, explicitly specify the 'neworder'
argument to gplots:::reorder.factor to prevent errors.
Other Changes:
- smartlegend() is now deprecated because the relative positioning
feature ('top', 'right') has been added to graphics::legend().
Calling smartlegend() will generate a warning.
- boxplot.n() and plot.lm2() are defunct have been removed. Use of
these functions will now generate an error.
- Update out-of-date URLs in man pages.
Release 2.16.0 - 2015-01-02
---------------------------
New Features:
- plotmeans() has a new argument, 'text.n.label' which specifies the
text used for labeling the number of elements in a group.
Bug Fixes:
- plotmeans() now respects (optional) graphical arguments captured in
'...' when drawing the x axis.
Release 2.15.0 - 2014-12-01
---------------------------
New features:
- Convert bandplot() to S3-method dispatch and add method for class
formula, so that 'bandplot( y ~ x, data=dataframe )' now works as
expected.
Other changes:
- heatmap.2() now uses a local *non-byte-compiled* copy of
plot.dengrogram, because the byte-compiled stats:::plot.dendrogram
uses a recursive algorithm that generates a 'node stack overflow'
error for deeply nested dendrograms and the node stack size cannot
be changed at execution time. Instead, tne local non-byte-compiled
gplots:::plot.dendrogram will trigger a recursion limit for such
dengrograms. heatmap.2() will detect this error and recommend that
the user increase the recursion limit (via,
e.g. 'options("expressions"=20000)' ) and rerun.
Release 2.14.2 - 2014-09-17
---------------------------
Bug Fixes:
- heatmap.2() was not respecting key.title=NA when density.info="none".
- Correct the man page for heatmap.2 to state that the default color
for 'notecol' is cyan.
- In heatmap.2(), modify default arguments to 'symbreaks' and 'symkey'
to make the logic more evident by replacing min(...) with
any(...). (The previous code executed properly, but relied on
implicit coercion of logicals to numeric, obscuring the intent.)
- Calling heatmap.2 with deeply nested dendrograms could trigger a
'node stack overflow' error. Now, this situation is deteceted, and
a message is generated indicating how to increase the relevant
recursion limit via options("expressions"=...).
Release 2.14.1 - 2014-06-30
---------------------------
Bug Fixes:
- Correct heatmap.2() bug in Colv dendrogram object dimension checking introduced
in 2.14.0. (Reported by Yong Fuga Li.)
Release 2.14.0 - 2014-06-18
---------------------------
Bug Fixes:
- heatmap.2(): Fix typo in heatmap.2() that caused an error when
'Rowv=FALSE'. (Reported by Yuanhua Liu.)
Enhancements:
- heatmap.2(): Add new 'reorderfun' argument to allow the user to
specify an alternative function to reorder rows/columns based on
row/column dendrogram. (Suggested by Yuanhua Liu.)
- heatmap.2(): Center margin labels.
- heatmap.2(): Check size of user-provided Rowv and Colv dendrogram
objects to ensure they match the dimensions of the data.
- Add references to man page for hist2d() and ci2d() to the new r2d2
package which implements an improved algorithm for 2-dimensional
emprical confidence regions.
Release 2.13.0 - 2014-04-04
---------------------------
Bug Fixes:
- heatmap.2 was not properly handling row trace reference line ('hline').
Patch submitted by Ilia Kats.
Enhancements:
- In heatmap.2, when the row or column trace is enabled, show the
corresponding reference line in the color key.
- In heatmap.2, a new 'extrafun' argument is provided that allows the
user to specify a function to be called before the function returns.
This allows the user to add additional plots to the page.
Release 2.12.1 - 2013-10-14
---------------------------
API Changes:
- boxplot.n() has been renamed to boxplot2() to avoid potential S3
method calling issues.
- plot.lm2() has been rename to lmplot2() to avoid potential S3 method
calling issues.
Enhancements:
- Add heatmap.2() parameters to control row and column label rotation
('srtRow', 'srtCol'), justification ('adjRow', 'adjCol'), and space
from plot edge ('offsetRow', 'offsetCol').
Bug Fixes:
- Fix error in in venn() when all groups contained the same number of TRUE cases.
- Correct error in overplot() when that occured when a group-category contained no
finite values.
Other Changes:
- Changes to overplot() to avoid warnings from upcoming enhancements to R CMD check.
- Move several packages from Depends to Imports or Suggests.
- Packages caTools and KernSmooth now have namespaces, so import
needed functions in NAMESPACE.
- Mark one example in manual page for ci2d 'dontrun' to avoid timing
warning in R CMD check.
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.
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
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