2016-03-30 warnes
* [r2122] R/plot.lowess.R: plotLowess() wasn't finding objects in
the caller's environment.
2016-03-28 warnes
* [r2121] DESCRIPTION, inst/NEWS: Update gplots version to 3.0.0.
* [r2120] man/heatmap.2.Rd: The 'layout' element of the list
returned from heatmap.2 is a named list, not a named vector.
* [r2119] man/gplots-deprecated.Rd: Used wrong comment character.
* [r2118] man/gplots-deprecated.Rd: Comment out arguments section
to avoid R CMD check warning.
2016-03-25 warnes
* [r2112] man/heatmap.2.Rd: Update URL for RColorBrewer
* [r2111] DESCRIPTION: Fix typos and quote uncommon words to make R
CMD check happy
* [r2110] DESCRIPTION, inst/ChangeLog, inst/NEWS: Update files for
gplots 2.18.0
* [r2109] NAMESPACE: Add imports recommended by R CMD check on
WinBuilder
* [r2108] man/heatmap.2.Rd: Add trailing slash to make R CMD
check's URL testing happy.
* [r2107] tests/heatmap2Test.Rout.save: Update test output to match
corrected messages
* [r2106] R/plot.venn.R: Warning message didn't have spaces between
words. Minor code reformatting.
* [r2105] R/lowess.R: Remove obsolete function to add '...' to
argument list for stats::lowess().
* [r2104] man/lowess.Rd, man/venn.Rd: Fix errors identified by R
CMD check
* [r2103] R/heatmap.2.R: Fix error when Rowv=FALSE or Colv=FALSE
* [r2102] man/gplots-defunct.Rd, man/gplots-deprecated.Rd: Fix
documenation issues identified by 'R CMD check'
* [r2101] man/venn.Rd: Correct discrepencies in man page
* [r2100] man/venn.Rd: Correct discrepencies in man page
* [r2099] man/lowess.Rd: Correct differences between calls on man
page and in code
* [r2098] R/lmplot2.R: Fix name of replacement functon in defuct
message generated by plot.lm2
* [r2097] man/lowess.Rd: Improve lowess() man page
* [r2096] NAMESPACE: Add plotLowess() and plot.lowess() to the
NAMESPACE
* [r2095] R/plot.lowess.R: Ensure lowess plot methods (invisibly)
return the lowess object.
* [r2094] man/lowess.Rd: Update man page for lowess to reflect new
lowess method for plot().
* [r2093] R/plot.lowess.R: Ensure extra arguments are properly
passed to the plot call.
* [r2092] R/heatmap.2.R: Corrected a bug causing "Error in
plot.new() : figure margins too large" to occur when 'key=FALSE'.
(Reported and patch provided by Sveinung Gundersen.)
2016-03-24 warnes
* [r2091] R/lowess.R, R/plot.lowess.R: Rename plot.lowess to
plotLowess to avoid confusions with plot() method for class
'lowess', create a plot() method for class 'lowess' and modify
the lowess.default() and lowess.formula() to add the 'lowess'
class to the returned object, along with a 'call' list element.
* [r2090] R/venn.R, R/vennMembers.R, man/venn.Rd: The
'intersections' attribute returned from venn() has been improved
to use set names instead of indicators, and is ordered from
simplest to most complex set interactions.
* [r2089] R/smartlegend.R, man/gplots-defunct.Rd,
man/gplots-deprecated.Rd: The smartlegend() function has been
made defunct and is no longer available.
* [r2088] R/lmplot2.R: Indentation changes
* [r2087] man/heatmap.2.Rd: Update heatmap.2() man page to reflect
addition of to the returned object.
* [r2086] R/lowess.R: Remove observations with missing values when
lowess is called using the formula interface.
* [r2085] R/heatmap.2.R: Add layout infromation to object returned
from heatmap.2() (patch provided by Jenny Drnevich).
* [r2084] DESCRIPTION: Correct spelling
2016-03-08 warnes
* [r2083] R/plot.lowess.R: Add function to plot points and lowess
using formula interface.
* [r2082] R/lowess.R: Remove old code for S-Plus and modernize
formula handling code.
* [r2081] R/heatmap.2.R: Set srtCol default if missing and colCol
is set
2016-02-26 warnes
* [r2080] R/venn.R: venn() now support matrix arguments.
* [r2079] R/angleAxis.R, man/angleAxis.Rd: New angleAxis() function
to create axis labels with rotated text.
* [r2078] R/heatmap.2.R: - heatmap.2() can now be used to plot
subsets of a previous heatmap.
- Remove stray 'browser()' debuggint statement from heatmap.2()
code.
- Decrease the granularity of the carpet in heatmap.2()'s color
key to
avoid visual artifacts.
2015-11-23 warnes
* [r2070] R/heatmap.2.R: Remove debugging print() statement.
2015-07-22 warnes
* [r2062] DESCRIPTION, R/heatmap.2.R, R/layout_set.R: Renamed
'test' directory to 'tests', commented out tests for lme4 which
has a changed API
2015-06-02 warnes
* [r2052] R/boxplot2.R: Defunct message for boxplot.n was
recommending the wrong function
2015-05-02 warnes
* [r2018] Rename 'trunk' to 'pkg' for compatibility with R-forge
2015-05-01 warnes
* [r2014] Again...
* [r2013] Update ChangeLog (again)
* [r2012] Summary: Correct man page name
* [r2011] Summary: Forgot to add \alias for smartlegend.
* [r2010] Remove leftover alias
* [r2009] Commit ChangeLog
* [r2008] Update NEWS again.
* [r2007] Mark boxplot.n and() plot.lm2() as defunct.
* [r2006] Make ballonplot.n() and plot.lm2() 'defunct'.
* [r2005] Update NEWS and ChangeLog again.
* [r2004] Summary: Punctuation.
* [r2003] Correct URLs in man pages.
* [r2002] Correct URLs in man pages.
* [r2001] Update NEWS again.
* [r2000] Improve package description.
* [r1999] Mark 'smartlegend' as deprecated
* [r1998] Summary: Mark smartlegend() as deprecated.
* [r1997] Summary: venn example used 'F' instead of 'FALSE'.
* [r1996] Update DESCRIPTION, NEWS, and ChangeLog again for gplots
2.17.0.
* [r1995] - heatmap.2: row traces could be plotted in the wrong
order.
* [r1994] - heatmap.2: column traces could be plotted in the wrong
order.
- heatmap.2: add support for plotting sub-clusters of the full
row and
column dendrograms
2015-04-23 warnes
* [r1955] Update NEWS and ChangeLog
* [r1954] In heatmap.2(), the color key now properly handles color
breaks that
are not equally spaced. (Issue reported by Tim Richter-Heitmann.)
* [r1948] - plotCI() was not properly respecting the 'type='
argument. This has
been corrected.
* [r1947] - Remove stray browser() call from overplot()
* [r1943] Explicitly specify argument to gplots:::reorder.factor to
prevent error.
* [r1942] - The returned object from venn() now includes a
'interesection'
attribution containing a list of which items are in each set
intersection. This can be turned off by settting
'intersection=FALSE'.
* [r1941] Patch submitted by Ilia Kats:
- easily extract and plot subclusters from a big heatmap using
the
same colorkey, by passing a dendgrogram 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. This is useful
if
one wants to plot several subclusters as different panels in a
paper, but maintain consistent color coding.
- Improves the behavior of the color key axis labels, as they now
honor par("cex") and par("cex.lab").
* [r1940] In heatmap.2() split calls to distfun() and hclustfun()
into separate steps to make debugging easier
2015-04-22 warnes
* [r1931] Update DESCRIPTION, ChangeLog, and NEWS for gplots 2.17.0
* [r1930] heatmap.2: add new 'colRow' and 'colCol' arguments to
control the color of row and column text labels
2015-04-06 warnes
* [r1916] Add ChangeLog files to repository
2015-01-02 warnes
* [r1913] Update for gplots release 2.16.0.
* [r1912] Change default group count lable back to 'n='.
* [r1911] - plotmeans: Pass optional graphical arguments captured
in '...' axis function
used to draw the x axis.
- plotmeans: Add an new argument 'text.n.label' to specify the
text
used for labelingthe number of elements in a group.
* [r1910] - Remove S-Plus-specific code
- Simplify model frame code
2014-12-03 warnes
* [r1909] Update stored test output to account for new startup
message from KernSmooth package
* [r1908] Fix package title capitalization.
2014-12-02 warnes
* [r1907] Add descrioption of node stack overflow issue and
work-around.
* [r1906] Move '...' argument to bandplot.formula to match man
page.
* [r1905] plot.dendrogram isn't exported by gplots, so it must be
referenced using the ':::' notation.
* [r1904] Man page fixes.
* [r1903] Add exports of new bandplot methods to NAMESPACE file.
* [r1902] Code cleanup.
* [r1901] Simplify model.frame code for bandplot.formula.
2014-12-01 warnes
* [r1900] Update for 2.15.0
* [r1899] Convert bandplot to S3-method dispatch and add method for
class formula.
* [r1898] Improve whitespace
2014-09-17 warnes
* [r1895] Minor reformatting.
* [r1894] Explicitly reset namespace for dendrogram functions
copied from stats.
* [r1893] Update DESCRIPTION and NEWS for gplots 2.14.2
* [r1892] To work around recursion limit issues triggered by deeply
nested
dendrograms, (1) create a local *intepreted* copy of
stats:::plotNode(), (2) detect recursion limit error message
within
heatmap.2() and generate a more user-friendly message.
* [r1891] Add test case for exceeding recursion limits when
plotting deeply nested dendrograms
* [r1890] heatmap.2 was not properly handling integer vectors for
Rowv and Colv.
* [r1889] key.title=NA was not being honored when density.info=NA.
2014-09-16 warnes
* [r1888] Add plotNode code to allow modificaiton of algorithm from
recursive to iterative for the purpose of avoiding node stack
overflow.
* [r1887] - Correct statement of default color for 'notecol'
argumemt to '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.)
2014-06-30 warnes
* [r1823] Fix typo in dendrogram size checking code.
2014-06-19 warnes
* [r1822] Fix typo 'ColInd' --> 'colInd'.
* [r1821] Update for gplots 2.14.0
2014-06-17 warnes
* [r1820] - Document new 'key.title', 'key.xlab', 'key.ylab',
'key.xtickfun',
'key.ytickfun', 'key.par' arguments to heatmap.2 (belated
commit).
- Document new 'reorderfun' argument to heatmap.2.
* [r1819] Allow user to specify function used to reorder based on
the dendogram
via a new 'reorderfun' argument. Suggested by Yuanhua Liu.
* [r1818] Fix typo in heatmap.2() reported by Yuanhua Liu.
2014-06-05 warnes
* [r1817] Check size of Rowv and Colv dendogram objects to ensure
they matches data.
2014-04-17 warnes
* [r1812] Add see also to r2d2::freq2d.
* [r1811] Add reference to r2d2::conf2d.
2014-04-09 warnes
* [r1802] Add padj=0.5 to better align margin labels.
2014-04-05 warnes
* [r1781] Update NEWS
* [r1780] Add 'extrafun' argument to heatmap.2 to allow the user to
perform
additional customization by providing a function to be called
before
heatmap.2 exits.
2014-04-04 warnes
* [r1779] Update for gplots 2.13.0
* [r1778] Fix handling of row trace (hline). Bug report and patch
provided by Ilia Kats.
2013-10-21 warnes
* [r1744] Handle 'ask' argument in lmplot2 function proper, rather
than in (depreciated) plot.lm2 wrapper.
* [r1743] Correct release number
* [r1742] Handle 'ask' argument in lmplot2 function proper, rather
than in (depreciated) plot.lm2 wrapper.
* [r1741] Fix typo
2013-10-15 warnes
* [r1740] Add boxplot2 and lmplot2 to NAMESPACE
* [r1739] Update for gplots release 2.12.1
* [r1738] Rename boxplot.n to boxplt2 and plot.lm2 to lmplot2
* [r1737] Make lmplot2 manual page from plot.lm.2 manual page.
* [r1736] Make boxplot2 manual page from boxplot.n manual page.
* [r1735] Create deprecated man page from boxplot.n man page
2013-10-12 warnes
* [r1734] Update NEWS with latest changes
* [r1733] Mark one example dontrun to avoid --as-cran warning.
2013-10-11 warnes
* [r1732] Allow standard S3 method handling to locate the correct
function.
* [r1731] Fix error when a subgroup contains no finite values
* [r1730] Update test output
* [r1729] Move several packages from Depends to Imports, Suggests
* [r1728] Use gdata::nobs in example
* [r1727] caTools and KernSmooth now have namespaces, so import
from them.
* [r1726] Update files for gplots 2.12.0
* [r1725] Update files for gplots 2.12.0
* [r1724] Add parameters to control row and column label
positioning, rotation, justification, and offset.
* [r1723] Fix bug in getVennCounts.data.frame when number of TRUE
cases in each variable are equal.
2013-06-28 warnes
* [r1680] Update PDF file, including new email addresses
2013-06-27 warnes
* [r1679] Update for gplots 2.11.3
* [r1678] Update for release 2.11.3
* [r1677] Update with tests for only 1 row/column separator
* [r1676] Fix typo
* [r1675] Add test for one row/column separator
* [r1674] Add more in-line comments
* [r1673] Modify sinkplot to use a local environement to store its
information instead of the global environment.
2013-03-24 warnes
* [r1647] Update news for release 2.11.2
* [r1646] Add ci.width argument to barplot2() to allow varying the
length of the 't' at the end of confidence interval bars.
* [r1642] Update for release 2.11.2
* [r1641] Update manual page for lowess.default() to match changed
argument list for lowess() in R 3.0.0
2012-12-14 warnes
* [r1631] Fix typo: warn() instead of warning().
* [r1630] Fix syntax of VignetteIndexEntry in venn.Rnw.
* [r1629] Add generated vignette pdf.
* [r1628] Add required VignetteIndexEntry metadata to venn vignette
code.
* [r1627] Update DESCRIPTION and NEWS for release 2.11.1.
* [r1626] Improve venn() to work with PDF and Sweave/pdflatex.
Provide a vignette for venn().
* [r1625] Fix error in processing the colsep argument to heatmap.2.
* [r1624] Clarify that plotmeans is intended for a *continuous*
outcome based on
a *factor* grouping level.
* [r1623] Replace corrupted BalloonPlot.pdf file and remove svn
properties that were causing it to be corrupted.
2012-06-08 warnes
* [r1558] Update NEWS for 2.11.0 release.
* [r1557] Fix R CMD check warnings.
* [r1556] Move incorrectly placed closing brace.
2012-06-07 warnes
* [r1555] Object returned by hist2d() has been changed:
- $x and $y now contain the n midpoints of the bins in each
direction
- $x.breaks, $y.breaks now contain the n+1 limits of the bins in
each direction
The function print.hist2d() has been updated appropriately.
* [r1554] Correct error in handling binning: (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.
* [r1553] Add default value for lwd argument to plotmeans()
2012-05-31 warnes
* [r1533] Properly mark up S3 method.
2011-12-09 warnes
* [r1519] Add 'lwd' (linewidth) to arguments handled by plotmeans.
2011-09-02 warnes
* [r1505] Update NEWS for release 2.10.1.
* [r1504] Increment version counter.
* [r1503] Add necessary alias statment to man files for for
'hist2d' and 'ci2d'
print methods.
* [r1502] Fix naming error
* [r1501] Provide print() methods for 'hist2d' and 'ci2d' objects.
* [r1498] Correct dependence on R >= 2.10
2011-09-01 warnes
* [r1491] - Correct issues in ci2d() man page.
* [r1490] - Comment out import from KernSmooth in NAMESPACES, since
KernSmooth
doesn't provide a namespace.
- Update a test output.
* [r1489] - Update NEWS file and correct version number
* [r1488] - Depend on KernSmooth package. Increment version number.
* [r1487] - Depend on KernSmooth package and import 'bkdeD2' and
'dpik'.
* [r1486] Improvements to ci2d():
- Add option to utilize KernDensity::bkde2D to estimate the 2-d
density (now the default).
- Add option to display points for original data on generated
plots
- Name elements of returned contour list according to the
significance
level to make it easier to select desired contours.
- Improve handling of x and y labels
* [r1485] Remove log tag and comments from top of the file.
2011-08-26 warnes
* [r1478] Update NEWS for 2.10.0 release
* [r1477] Add dependency on R>= 2.10 to handle compressed Rda data
file.
* [r1476] Compress rtPCR example data set to make distributed
package smaller.
* [r1475] Remove '1.0' confidence line from
ci2d(..,show="contour").
2011-08-25 warnes
* [r1474] - Add 'ci2d()' to compute 2-dimensional emipirical
confidence interval.
- Fix parse error in help page for 'rich.colors()'.
2011-08-16 warnes
* [r1473] Update DESCRIPTION file for 2.8.1.
* [r1472] Add 'alpha' argument to rich.colors() to control
transparency.
* [r1471] Accellerate hist2d by replacing for() loop with tapply(),
and allow user to specify summary function applied, per
suggestion by Peter Hagedorn (PHA -at- santaris -dot- com).
2011-05-02 arnima
* [r1470] Added argument 'alpha' and removed argument 'rgb' in
rich.colors()
2010-12-13 warnes
* [r1463] Correct error that arises when data includes NA values,
identified by Melissa Key
2010-06-11 warnes
* [r1446] Fix errors detected by R CMD check
* [r1445] Fix errors detected by R CMD check
* [r1444] Use 'TRUE' instead of 'T' for true in venn man page
* [r1443] Update for gplots 2.8.0
* [r1442] Moved baseOf() into a separate file
* [r1441] Update Greg's email address
* [r1440] - 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
2010-02-17 warnes
* [r1420] Improve performance of hist2d thanks to suggestion by
Joerg van den Hoff.
2010-01-22 arnima
* [r1372] Renamed files rich.color.* to rich.colors.* and renamed
rich.colors args
2009-11-16 arnima
* [r1367] Minor reformatting only.
2009-11-12 warnes
* [r1365] Correct bug reported by Alan Yong: plotmeans() crashed
when 'bars=FALSE'.
2009-10-22 warnes
* [r1364] Fixed typo in bug fix.
* [r1363] Update NEWS and DESCRIPTION for gplots 2.7.3
* [r1362] Fix transposed display of data (but not labels) in
heatmap.2 when symm=TRUE
2009-10-12 warnes
* [r1361] Update version number to 2.7.2, 2.7.1 was already up but
apparently DESCRIPTION wasn't commited with change.
2009-10-10 warnes
* [r1360] Various minor changes to remove new R CMD CHECK warnings.
* [r1359] Update DESCRIPTION and NEWS file for 2.7.1
* [r1358] Fix bug reported by Ken Lo: col2hex had blue and green
components swapped.
2009-05-08 warnes
* [r1324] Add test of using a dendrogram created by heatmap() with
heatmap.2()
* [r1323] heatmap.2: handle NA for RowV or ColV the same way as
NULL
* [r1322] Fix typo
* [r1321] Update NEWS for release 2.7.0
* [r1320] We don't want the Changelog in svn, since it is
autogenerated from svn logs!
* [r1319] Update Greg's email address to
'greg@random-technologies-llc.com'
* [r1318] plotCI now properly handles 'NULL' and 'NA' values for
ui, li, uiw, and liw.
* [r1317] heatmap.2: Add option to create breakpoints symmetric
around 0, provide additional information in the return value
* [r1316] Fix Rd syntax error
2009-04-22 warnes
* [r1315] VADeaths data set has move to dataset package
2008-08-14 warnes
* [r1302] balloonpot() was incorrectly displaying warning about z
values below 0 when scale.method="relative". Fixed.
2008-08-07 warnes
* [r1301] Update DESCRIPTION NAMESPACE and NEWS for 2.7.0 release
2008-06-16 warnes
* [r1296] Add TODO list to gplots
2008-05-20 warnes
* [r1274] Update man page to match recent changes to plot.lm2()
* [r1273] More work on documentation for venn()
* [r1272] Fix code/doc mismatch due to recent changes to bandplot()
* [r1271] Add Venn Diagram plot submitted by Steffen Moeller
2008-05-07 warnes
* [r1264] Improve performance of bandplot by calculating running
standard deviation using caTools::runsd() instead of (ver slow)
window() call. In addtion, the standard deviations are now only
calculated once, rather than once for each band.
* [r1263] Improve performance of plot.lm for large lm objects by
using fitted() instead of predict() to get y-hat
2008-05-05 warnes
* [r1262] Use caTools's runsd in bandplot for a dramatic speedup
for large data
* [r1261] Add import of gtools::reorder.factor for ballonplot man
page
* [r1260] balloonplot: Add option to scale balloons so
[min,max]->[0,1] (relative) or so [0,max] <- [0,1] (absolute)
2008-04-07 warnes
* [r1254] Fix typo in barplot2() man page
* [r1253] Updates for gplots 2.6.0
* [r1252] Add ability to control location of individual heatmap.2
components
2008-03-27 warnes
* [r1251] Fix bug in handling rowsep, per suggestion by Steven
Paugh
2008-01-04 warnes
* [r1238] Fix examples for overplot()
2008-01-02 warnes
* [r1237] Update Marc's email address
2007-12-20 warnes
* [r1235] Two letter clarification of help text for heatmap.2()
* [r1234] Restore plot layout at end of ooplot() example
2007-11-06 warnes
* [r1222] Remove extraneous closing brace in the hist2d
documentation file
2007-11-05 warnes
* [r1221] Fix typo in NEWS: col2hex() is the new function, not
col2rgb() which is part of grDevices
2007-11-02 warnes
* [r1219] Updates for gplots 2.5.0
* [r1218] Update saved test output due to changes in how R reports
warnings
* [r1217] Create soft links of gmodels/ChangeLog ->
gmodels/inst/ChangeLog, and gmodels/NEWS -> gmodels/inst/NEWS for
my convenience
* [r1216] Move actual ChangeLog and NEWS files to gmodels/inst so
they will be copied into the installed R package area
* [r1215] Fix code/doc mismatches
* [r1214] Update plot.lm2 to match changes made to bandplot
2007-11-01 warnes
* [r1213] in textplot(), convert tab characters to spaces before
processing to avoid problems with computing height and width of
text including tabs when using pdf()
* [r1212] Minor reformatting of overplot code and docs
2007-10-22 warnes
* [r1196] Clarify GPL version
2007-08-14 warnes
* [r1141] Correct error in balloonplot when z contains NA values.
* [r1140] Augment balloonplot() with control of character size and
color for text and label items
* [r1139] Correct balloonplot.default to properly show specified x
and y axis labels when explicitly provided
2007-03-09 ggorjan
* [r1073] use of \method in Rd markup - issues a warning with
_R_CHECK_RD_STYLE_=TRUE env. variable with R 2.5.0
2007-02-08 warnes
* [r1052] Bump version number
* [r1051] Update documentation for textplot()
* [r1050] Add col2rgb() function to convert color names to rgb hex
codes
* [r1049] Add paramaeters 'col.data', 'col.rows', and 'col.columns'
to
textplot.matrix to allow specification of the color of the matrix
data, rows, and columns.
* [r1048] Add parameters to control line width and line type.
2006-11-14 ggorjan
* [r1012] Removed executable property
2006-11-14 warnes
* [r1010] Update output file to match (trivial) changes in the test
code.
* [r1008] Update ChangeLog and NEWS files for release 2.3.2.
* [r1007] Update version number
* [r1006] Update version number and maintainer
* [r1005] Correct problem with labeled correlation matrix example.
Thanks to Jean Vidal for reporting the error..
2006-08-02 warnes
* [r977] Update my email address
2006-06-26 nj7w
* [r967] Fixed a bug which displayed warnings when Rowv and Colv
were specified as dendrograms
2006-03-10 warnes
* [r937] Remove code that added a local path
2006-03-09 nj7w
* [r935] Added the correct library path where gplots is installed
locally and corresponding .save file
* [r934] Updated the tests file
* [r933] Removed the condition Colv != Rowv as it has already been
taken care of
* [r932] Deleted rtPCR.rda from the main directory
* [r931] Added ChangeLog
2006-03-07 nj7w
* [r919] Updated ChangeLog and NEWS
* [r918] Added the tests and fixed corrupted files
* [r917] Replaced the corrupted rtPCR.rda file in data directory
* [r916] Removed the corrputed tests directory
* [r915] Replaced the corrupted rtPCR.rda file in data directory
2006-03-03 nj7w
* [r914] Updated the code and man page to make sure the Rowv and
Colv values are properly handled
2006-03-02 warnes
* [r908] Adjust row total placement to adjust for width of the
totals
* [r907] Row totals in ballonplot were in reverse order. Fixed.
2006-02-23 nj7w
* [r899] Add ability to scale the color key using the new 'keysize'
argument.
* [r898] Add tests for heatmap.2
* [r897] Move heatmap and ballonplot paper source materials to
their respective cvs modules
* [r896] Moved balloonplot paper materials to BallonPlotPaper cvs
module
* [r891] Remove heatmap paper files and move them to the
HeatmapPaper cvs module.
* [r888] Added figures for heatmap2 paper
* [r887] Added the .Rda files for the heatmap2 paper
* [r886] Added the source - (tex file) of the heatmap paper
* [r885] Added the code for the figures of heatmap paper
2006-02-21 nj7w
* [r884] Minor updates to heatmap.2 - fixed Rowv, Colv and
dendrogram behaviour. Now Rowv=NULL or FALSE both imply no
dendrogram computation.
2006-01-12 warnes
* [r844] more updates
* [r843] Add Biometrica bibliography style file
* [r842] A little more.
* [r841] Updates to respond to referee.
2006-01-12 nj7w
* [r840] Added references
2005-12-13 nj7w
* [r811] Fixed Nitin's company name
* [r809] Updated NEWS and removed ChangeLog
2005-12-12 nj7w
* [r802] Fixed bug in plotmeans - based on Stefano Calza's
suggestion
2005-12-07 nj7w
* [r787] Updated version number
* [r786] Added plot.lm
* [r785] Changed the default grey colors to heat colors, if height
is matrix
* [r784] Changed the default greay colors to heat colors, if height
is matrix
2005-12-06 nj7w
* [r783] Fixed minor error in documentation of barplot2
2005-12-02 warnes
* [r777] Remove .Alias calls, since .Alias is defunct.
2005-12-01 nj7w
* [r776] Updated Greg's email address
2005-11-23 nj7w
* [r764] Updated Figure 2 colors
2005-11-18 warnes
* [r743] Latest version of the pdf files
* [r742] Nitin works for the Cambrige Group, not Pfizer.
* [r741] Minor text rewording.
* [r740] More edits.
* [r739] Recent changes to align row totals with the overall total
broke how
the marginal cumulative fractions were displayed. This patch
fixes
the problem.
* [r737] - Update documentation for balloonplot to match the latest
code.
- Correct spelling of 'show.zeroes' to 'show.zeros'
* [r736] More changes: colorpanel now allows only 2 colors to be
specified if
no 'middle' color is desired.
2005-11-17 warnes
* [r735] Allow user to control removal of duplicate entries in
balloonplot.
* [r734] Extend colorpanel to handle just two-colors in addition to
three.
2005-11-09 nj7w
* [r733] Updated the pdf file
* [r732] Updated the changes
* [r731] Modified figure 4
* [r730] Updated code
* [r729] Modified figure 3
* [r728] Modified figure 2
* [r727] Modified figure 1
2005-11-08 nj7w
* [r726] Updated Greg's email
2005-11-07 nj7w
* [r725] Minor modifications to fit the code properly on pdf
2005-11-07 warnes
* [r724] Add R code that generates plots
* [r723] Add figures to CVS
* [r722] Text changes
2005-11-04 warnes
* [r721] Fix some alignment issues.
* [r720] Remove Table.pdf since it is no longer needed
* [r719] Nitin's Changes
* [r718] Add figure plots
* [r717] Fix paths
2005-10-20 nj7w
* [r705] added the eps version of figures
* [r704] Updated BallonPlot.pdf
* [r703] Removed Old Figure
* [r702] Added the new figure - for total popluation - Balloonplot
* [r701] Modified the BallonPlot article
* [r700] Added references
2005-10-19 arnima
* [r697] The last example now displays the correct heat.colors.
Default 'palette' argument is now a single string, not a vector.
* [r696] Default 'palette' argument is now a single string, not a
vector.
2005-10-14 warnes
* [r694] Formatting fixes:
- Handle multiple row or column category variables
- Separate rows/columns of category labels by lines
- Fix handling of 'cumsum' plots on row/column labels
- Improve display of row/column sums
2005-10-13 warnes
* [r693] Add example using Titanic data that exercises the
multi-factor
display.
2005-10-11 warnes
* [r692] Initial changes to allow multiple x and y factor
variables. Yet to
be done: 1) remove extra 'boxes'. 2) omit duplicated values
2005-10-04 warnes
* [r691] more minor fixes
* [r690] fix spacing
* [r689] Inlcude Rnews.sty
* [r688] Some textual edits.
2005-10-03 nj7w
* [r687] Added figures for the R-News Article
2005-09-29 nj7w
* [r680] Updated the documentation - added the name of the person
who asked the question
* [r679] Added R-news article
2005-09-12 nj7w
* [r671] Updated Greg's email
* [r670] Updated version of balloonplot - by Romain Francois
<francoisromain@free.fr>
2005-09-09 nj7w
* [r669] Updated the version and ChangeLog
* [r668] Changes in ballon plot based on Romain Francois
(francoisromain@free.fr) suggestions
2005-09-06 nj7w
* [r666] Updated package dependencies
* [r665] Added NEWS
2005-09-02 nj7w
* [r655] Added ChangeLog
2005-08-31 nj7w
* [r644] Added DESCRIPTION file
* [r643] removed DESCRIPTION.in
2005-06-09 nj7w
* [r625] Updating the version number, and various help files to
synchronize splitting of gregmisc bundle in 4 individual
components.
* [r624] Changes based on Marc Schwartz's suggestions to handel 0's
and NA's appropriately.
2005-05-13 nj7w
* [r621] 1) Using dQuote.ascii function in read.xls as the new
version of dQuote doesn't work proprly with UTF-8 locale.
2) Modified CrossTable.Rd usage in gmodels
3) Modified heatmap.2 usage in gplots.
2005-04-04 warnes
* [r603] Explicitly reference package containing lowess.formula in
panel.overplot(). This should fix the error reported by Troels
Ring
<tring@gvdnet.dk>.
2005-02-26 nj7w
* [r565] *** empty log message ***
2005-02-25 warnes
* [r563] Integrate changes submitted by Arni Magnusson
* [r559] Add dependency imports from 'stats' package.
2005-02-22 warnes
* [r555] Fix problem in passing graphical parameters (xlim,etc).@
2005-02-08 warnes
* [r541] Improve package title.
* [r540] Ignore missing values when computing symmetric range.
2005-02-02 warnes
* [r530] Add more extensive example.
2005-01-14 warnes
* [r516] Code can be simplified because R now supports selecting a
fixed width font.
2005-01-12 warnes
* [r515] Add dependency on R 1.9.0+ to prevent poeple from
installing on old
versions of R which don't support namespaces.
2004-11-30 warnes
* [r495] 1. Add new parameters for controlling color key:
- If `symkey==TRUE', the color key will be made symmetric about
0.
- The `densadj' parameter can be used to modify the smoother
width
(see the `adjust' parameter under `help(density)') for the
density
plotted in the key.
2. Fix handling of rowsep/colsep.
3. Vector of length 2 giving the width (colsep) or height
(rowsep) the separator box
drawn by colsep and rowsep as a function of the width (colsep) or
height (rowsep) of a cell.
4. Appropriate changes to the corresponding help page, plus some
minor formatting changes.
2004-11-03 warnes
* [r474] Fix bugs in layout of cell notes. They were being plotted
top down
rather than bottom up. Further reordering of the x matrix didn't
also reorder the notes. Both issues should now be resolved.
2004-09-27 warneg
* [r461] Updated to pass R CMD check.
2004-09-03 warneg
* [r453] Provide explicit package for call to nobs.
* [r452] Fix typos.
* [r446] initial bundle checkin
2004-09-02 warneg
* [r442] Initial revision
2004-07-29 warnes
* [r426] Integrate changes from the version of plotCI maintained by
Martin Maechler.
2004-06-30 warnes
* [r393] Remove commented-out code.
* [r392] Fixed text size calculations
2004-06-28 warnes
* [r391] - Default 2-d color set to grey as in (v2.0.0) r-devel
- The default (v1.9.1) barplot method now handles vectors and 1-d
arrays
(e.g., obtained by table()) the same, and uses grey instead of
heat color palettes in these cases. (Also fixes PR#6776.)
- Updated to reflect the addition of 'offset' argument in base
- Fix bug in stacked barplots, which would not be plotted
properly
2004-06-24 warnes
* [r385] Add ability to specify color of NA cells.
2004-05-27 warnes
* [r349] Fix spelling error.
2004-05-26 warnes
* [r347] One more fix to get it right.
* [r346] Use triple-colon operator ':::' to access plot.formula
from the graphics package.
* [r344] Replace 'F' by 'FALSE' to pass R CMD check.
2004-05-25 warnes
* [r338] Work around bug in R 1.9.X due to plot.formula() not
having the same
arguments as plot().
* [r336] Add rich.colors() submitted by Arni Magnusson
<arnima@u.washington.edu>.
* [r328] ??
2004-05-24 warnes
* [r324] Modified to use invalid() to check arguments instead of
missing().
This fixes some build errors under R-1.9.0-Patched.
2004-04-22 warnes
* [r319] Integrate changes from Lodewijk Bonebakker
<bonebakker@comcast.net>
2004-04-13 warnes
* [r318] Add ability to space points along 'y' direction.
2004-04-02 warnes
* [r313] Fixed smartlegend() positioning when x and/or y axis are
log-scale.
2004-03-30 warnes
* [r311] - Fix bug in textplot() reported by Wright, Kevin
<kevin.d.wright@pioneer.com>.
2004-03-26 warnes
* [r305] Update to match changes in textplot() code.
* [r304] Remove Windows EOL characters.
* [r302] - Remove some commented-out code.
- Remove cvs log tag.
* [r300] Misc changes.
2004-02-17 warnes
* [r290] Minor fix to ooplot documentation.
* [r289] Integrate ooplot updates provided by Lodewijk Bonebakker
<bonebakker@comcast.net>
2004-02-02 warnes
* [r287] - Add colorpanel function, which generates a smoothly
varying band of
colors over a three color range (lo, mid, high).
2004-01-21 warnes
* [r283] - Correct arguments to halign to match code.
* [r281] Track R 1.9.0's move of 'lowess' from the base package to
the (new)
stats package.
* [r279] - Fix sinkplot() example by replacing 'T' with 'TRUE'.
* [r278] - Add some more details to the ooplot() documentation. The
documentation is *not* complete.
* [r277] - Mark sprint() as depreciated.
- Replace references to sprint with capture.output()
- Use match.arg for halign and valign arguments to
textplot.default.
- Fix textplot.character so that a vector of characters is
properly
displayed. Previouslt, character vectors were plotted on top of
each
other.
2004-01-19 warnes
* [r276] New function sinkplot(), as requested on R-devel by Kevin
Wright
<kwright@eskimo.com> in
https://www.stat.math.ethz.ch/pipermail/r-devel/2004-January/028483.html.
2004-01-15 warnes
* [r274] Add initial code and docs for ooplot() function submitted
by Lodewijk
Bonebakker <bonebakker@comcast.net>.
2003-12-03 warnes
* [r253] - match function argument defaults with 'usage'
* [r252] - Fix buglets in heatmap function
- Make a slight enhancement to the example code.
2003-12-02 warnes
* [r251] Integrated some suggestions from Sean Davis
<sdavis2@mail.nih.gov>.
* [r250] - Make final example use 16 colors instead of 8. This
looks nicer.
* [r248] - Remove '%' character from example code to avoid errors.
* [r247] - Add '...' parameter to call to text to allow user to
control size/color/etc.
2003-12-01 warnes
* [r246] - updated to match changes to barplot() in base.
* [r245] - Renamed rtPCR.Rda to rtPCR.rda so that R will properly
load the file
when data(rtPCR) is executed.
* [r243] - Follow patches applied to barplot() in base.
2003-11-24 warnes
* [r242] Fix unbalanced braces.
* [r240] Fix errors reported by R CMD check.
2003-11-21 warnes
* [r239] Added missing closing brace.
* [r238] Initial addition of these files. Used in examples of
overplot().
* [r236] Applied my enhancements to the heatmap() code from R
1.8.0, and added
documentation of these changes.
* [r235] - Discovered that axis(N) does the right thing without
needing to be
given location for tick marks. This allowed simplification of the
code.
- Minor other changes for distribution
- Addition of overplot.Rd documentation.
* [r231] - Integrated my extensions into the R 1.8.0 version of
heatmap.
- Add Rd documentation.
2003-11-19 warnes
* [r228] Remove extranious NULL that confused R CMD check.
2003-11-18 warnes
* [r226] - Tiny fix to remove R CMD check error.
* [r225] - Added missing closing brace.
* [r224] - Convert from MS-Dos to Unix line endings.
- Reformat to 80 columns.
2003-11-10 warnes
* [r220] - Add files contributed by Arni Magnusson
<arnima@u.washington.edu>. As well as some of my own.
2003-08-19 warnes
* [r219] - Copy of local changes.
* [r218] - Checkin before re-integrating local changes.
2003-06-19 warnes
* [r201] - Added enhanced heatmap function.
2003-06-09 warnes
* [r200] - Add help text for smartlegend.
* [r199] - New function smartlegend().
2003-04-22 warnes
* [r191] - Fixeed warning messing caused when 'connect' is a
vector.
* [r187] Update from Marc Schwartz, modified by Gregory Warnes:
- Modified dim() checks for 'ci.l' and 'ci.u' against 'height'
to remove R v1.7.0 if() based error msgs for vector conditions.
2003-04-04 warnes
* [r182] - Change occurences of 'T' to 'TRUE'
* [r179] - Updated to match changes in textplot function:
- Added textplot.character
- Renamed arguments "col.margin" and "row.margin" to "cmar", and
"rmar" so that specifying "col='red'" is possible.
- Fixed R CMD check errors
- Improve comments in example
- Add textplot.matrix example
* [r178] - Added textplot.character to handle character strings.
- Moved test for vector and matrix arguments to textplot.default.
- Renamed arguments "col.margin" and "row.margin" to "cmar", and
"rmar" so that specifying "col='red'" is possible.
2003-04-02 warnes
* [r175] - Added textplot function and friends, as well as
documentation.
2003-03-08 warnes
* [r171] - Forgot to update arglist in \usage section.
* [r169] - Added parameters for rotation of and amount of space
allocated for
the row and column labels.
2003-03-07 warnes
* [r168] - Minor changes to code to allow the package to be
provided as an
S-Plus chapter.
* [r167] - Add 'NULL' as the last element of if statement that
defines
lowess.default so that when the file is sourced, S-Plus doesn't
display the function definition.
* [r166] - Specify where the defualt lowess function should be
found.
- Use getFunction in S-Plus instead of 'get'
2003-01-30 warnes
* [r159] - Added argument 'add' to allow for the addition of a
barplot to an
existing graphic. Default is FALSE
2003-01-20 warnes
* [r156] - Updated balloonplot help page.
* [r155] - Updated wapply.R to allow specification of evaluation
points when
method is 'width' or 'range' using the 'pts' argument.
- Updated wapply.Rd to add 'pts' argument
- Fixed typos, spelling errors, gramatical errors and lack of
clarity
in wapply.Rd help text.
2003-01-03 warnes
* [r154] - Initial checkin of balloonplot functions and
documentation.
* [r153] - Added reference to and comparison example of
sunflowerplot.
- Added code to put example plots on same plot window using
par(mfrow=...).
2003-01-02 warnes
* [r150] - Changed assignment statements that used "=" to "<-" to
avoid syntax
errors in older versions of the S language.
* [r149] - Added wrapper code so that R-specific fiddling won't be
executed
under S-Plus.
* [r147] - Renamed first parameter to match qqnorm generic.
* [r146] Added additional help text from Kjeitl.
2002-12-31 warnes
* [r145] Initial checkin of qqnorm.aov function and documentation
submitted by
Kjetil Halvorsen <kjetilh@jupiter.umsanet.edu.bo>.
2002-11-04 warnes
* [r143] Updates from Marc Schwartz:
- Updated underlying code to be based upon the new barplot() in R
v1.6.1
- This now uses the 'axis.lty' and 'border' arguments
- In R v1.6.0, R Core introduced a new function called axTicks().
This is an R equivalent of the C code for CreateAtVector in
plot.c.
This now enables me to get the axis tick mark positions
consistently
when the 'height' related axis is either linear or log. Thus, I
can
now have consistent tick marks and can plot grid lines in either
situation. If 'plot.grid = TRUE' and 'grid.inc' is specified,
then
I still use pretty() to determine the tick marks and lines.
- This code now depends on R 1.6.0 or later.
2002-10-30 warnes
* [r139] - Commented out plot.lm() code since recent changes in R
have broken it.
2002-10-11 warnes
* [r131] - Fixed log scale errors in legend() call
2002-10-01 warnes
* [r130] - Added examples of using 'contour' and 'filled.contour'
for display.
2002-09-24 warnes
* [r121] - Changed digits=options("digits") which produces a list
of length 1
to digits=getOption("digits") which returns a vector of length
one.
The former was causing an error when passed to round().
2002-09-23 warnes
* [r119] - Fixed syntax errors in barplot2.Rd and CrossTable.Rd
- Fixed incorrect translation of 'F' (distribution) to 'FALSE' in
glh.test.Rd
* [r117] - Modified all files to include CVS Id and Log tags.
* [r116] - Added CrossTable() and barplot2() code and docs
contributed by Marc Schwartz.
- Permit combinations() to be used when r>n provided
repeat.allowed=TRUE
- Bumped up version number
2002-08-01 warnes
* [r114] - Corrected documentation mismatch for ci, ci.default.
- Replaced all occurences of '_' for assignment with '<-'.
- Replaced all occurences of 'T' or 'F' for 'TRUE' and 'FALSE'
with
the spelled out version.
- Updaded version number and date.
2002-04-09 warneg
* [r109] Checkin for version 0.5.3
2002-03-27 warneg
* [r107] Added "..." argument to lowess.default.
* [r106] - Added code to append "..." to the argument list of
lowess.default.
- Fixed a wrong default for f in lowess.formula. Was 3, but
should
have been 2/3.
2002-03-26 warneg
* [r104] - Changed methods to include '...' to match the generic.
- Updated for version 0.5.1
* [r100] Initial checkin.
2002-03-20 warneg
* [r94] - Changes to add compatibility with S-Plus 2000
* [r93] - Changes to add compatibility with S-Plus 2000.
* [r92] - Updated to work in S-Plus 2000 as well as R.
2002-03-05 warneg
* [r88] - Replace "T" with "TRUE". Problems arrive when there is a
variable named "T".
2002-02-20 warneg
* [r81] Minor changes, typo and formatting fixes.
* [r80] - Generalized to allow specification of the multiples of
the standard deviation levels to be plotted (0=mean, 1=1 sd, ..).
- Now (invisibly) returnes computed smooths.
2002-02-16 warneg
* [r78] Added bandplot documentation.
* [r77] - Fixed Bug: When method=="range", the absolute range of x
was being
used to compute the relative width instead of the (correct)
relative
range.
* [r76] - Corrected problem removing missing values: The missing
values of $x
and $y were being removed indepdendently, leaving an uneven
number
of points in the result.
2002-02-04 warneg
* [r74] - Add na.rm parameter and make the default TRUE.
* [r73] Initial checkin.
* [r72] - When err="x", 'col' was being used to plot bars, rather
than 'barcol'.
* [r71] - fixed typo, when err="x", lty was 'slty' causing an
error.
2001-12-12 warneg
* [r54] - Quoted underscore character in my email address.
- Added correct keyword.
* [r52] Added documentation for xaxt parameter.
* [r51] Updated to explicitly list control arguments to
lowess.formula.
* [r50] Initial checkin. Code copied from R source package and
extended.
2001-12-07 warneg
* [r46] Fixed an problem where \code was incorrectly delimited by
parens
rather than curly brackets.
* [r42] Initial checkin.
* [r41] - Added cvs tags.
* [r40] - Leave first point at center, rather than shifting by s/2
to the left. This looks better when there are more than 2
'spaced' points.
2001-12-05 warneg
* [r33] - Added ability to use the t-distribution to compute
confidence
intervals. This is controlled using the 'use.t' parameter.
* [r31] - Added documentation of use.t parameter.
* [r30] - Clarified how the width of the window is computed when
method="nobs".
* [r29] - Added a better default for "width" when method="nobs".
For this case,
width=max(5, length(x)/10).
- Allow omission of x values which result in missing y values via
'drop.na' parameter.
2001-10-26 warneg
* [r28] Added correct handling of 'xaxt="n"'.
2001-10-16 warneg
* [r27] Fixed unbalanced brace.
* [r26] Added minbar and maxbar parameters.
* [r25] Forgot to add minbar and maxbar to usage section.
* [r24] Added description of minbar and maxbar.
* [r23] - Added minbar and maxbar parameters
- Added cvs id and log tags to header
* [r22] Added cvs id and log tag to file header
* [r21] Added minbar and maxbar parameters.
* [r20] Added description of minsd parameter.
* [r19] Added minsd parameter.
2001-09-18 warneg
* [r18] Release 0.3.2
2001-09-01 warneg
* [r16] Release 0.3.0
2001-08-31 warneg
* [r15] Used wrong character in header (% instead of #). Fixed.
* [r14] Used wrong comment character (% instead of #) in header.
Fixed.
2001-08-25 warneg
* [r10] Initial checkin.
* [r9] Added CVS header.
* [r8] Initial Checkin
2001-05-30 warneg
* [r2] Initial revision
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