Thread: [R-gregmisc-users] SF.net SVN: r-gregmisc: [1008] trunk/gplots
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From: <wa...@us...> - 2006-11-14 18:09:04
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Revision: 1008
http://svn.sourceforge.net/r-gregmisc/?rev=1008&view=rev
Author: warnes
Date: 2006-11-14 10:07:31 -0800 (Tue, 14 Nov 2006)
Log Message:
-----------
Update ChangeLog and NEWS files for release 2.3.2.
Modified Paths:
--------------
trunk/gplots/ChangeLog
trunk/gplots/NEWS
Modified: trunk/gplots/ChangeLog
===================================================================
--- trunk/gplots/ChangeLog 2006-11-14 17:59:51 UTC (rev 1007)
+++ trunk/gplots/ChangeLog 2006-11-14 18:07:31 UTC (rev 1008)
@@ -1,200 +1,262 @@
+2006-11-14 17:56 warnes
+
+ * man/heatmap.2.Rd: Correct problem with labeled correlation matrix
+ example. Thanks to Jean Vidal for reporting the error..
+
+2006-08-02 22:21 warnes
+
+ * trunk/BalloonPlotPaper/BalloonPlot.pdf,
+ trunk/BalloonPlotPaper/BalloonPlot.tex,
+ trunk/MSOfficeUtil/DESCRIPTION,
+ trunk/PathwayModeling/thesispaper/slides.tex,
+ trunk/RMCMC/DESCRIPTION, trunk/RMCMC/man/make.density.Rd,
+ trunk/Rlsf/DESCRIPTION, trunk/Rlsf/man/lsf.numcpu.Rd,
+ trunk/Rlsf/man/lsf.parRapply.Rd, trunk/Rlsf/man/scat.Rd,
+ trunk/bwRF/DESCRIPTION, trunk/bwRF/man/RF.Rd,
+ trunk/exp.ssize/inst/doc/ssize.pdf,
+ trunk/exp.ssize/inst/doc/ssize.tex, trunk/fork/DESCRIPTION,
+ trunk/fork/man/exit.Rd, trunk/fork/man/fork.Rd,
+ trunk/fork/man/getpid.Rd, trunk/fork/man/kill.Rd,
+ trunk/fork/man/signame.Rd, trunk/fork/man/wait.Rd,
+ trunk/gdata/inst/doc/gregmisc.tex,
+ trunk/gdata/man/ConvertMedUnits.Rd,
+ trunk/gdata/man/aggregate.table.Rd, trunk/gdata/man/combine.Rd,
+ trunk/gdata/man/interleave.Rd, trunk/gdata/man/matchcols.Rd,
+ trunk/gdata/man/nobs.Rd, trunk/gdata/man/read.xls.Rd,
+ trunk/gdata/man/rename.vars.Rd, trunk/gdata/man/reorder.Rd,
+ trunk/gdata/man/trim.Rd, trunk/gdata/man/unmatrix.Rd,
+ trunk/gdata/man/upperTriangle.Rd,
+ trunk/gmodels/man/fast.prcomp.Rd,
+ trunk/gmodels/man/fit.contrast.Rd, trunk/gmodels/man/glh.test.Rd,
+ trunk/gmodels/man/make.contrasts.Rd, inst/doc/BalloonPlot.pdf,
+ man/balloonplot.Rd, man/bandplot.Rd, man/boxplot.n.Rd,
+ man/colorpanel.Rd, man/hist2d.Rd, man/ooplot.Rd, man/overplot.Rd,
+ man/plot.lm2.Rd, man/plotCI.Rd, man/plotmeans.Rd,
+ man/residplot.Rd, man/sinkplot.Rd, man/smartlegend.Rd,
+ man/space.Rd, man/textplot.Rd, man/wapply.Rd,
+ trunk/gregmisc/DESCRIPTION,
+ trunk/gregmisc/gregmisc/DESCRIPTION.standalone,
+ trunk/gregmisc/inst/doc/gregmisc.tex,
+ trunk/gtools/man/addLast.Rd, trunk/gtools/man/assert.Rd,
+ trunk/gtools/man/capture.Rd, trunk/gtools/man/combinations.Rd,
+ trunk/gtools/man/defmacro.Rd, trunk/gtools/man/dirichlet.Rd,
+ trunk/gtools/man/foldchange.Rd, trunk/gtools/man/invalid.Rd,
+ trunk/gtools/man/logit.Rd, trunk/gtools/man/mixedsort.Rd,
+ trunk/gtools/man/oddeven.Rd, trunk/gtools/man/permute.Rd,
+ trunk/gtools/man/quantcut.Rd, trunk/gtools/man/running.Rd,
+ trunk/gtools/man/scat.Rd, trunk/gtools/man/setTCPNoDelay.Rd,
+ trunk/nws/DESCRIPTION, trunk/qvalue/DESCRIPTION,
+ trunk/qvalue/man/print.qvalue.Rd, trunk/ssize/DESCRIPTION,
+ trunk/ssize/man/pow.Rd: Update my email address
+
+2006-06-26 21:08 nj7w
+
+ * R/heatmap.2.R: Fixed a bug which displayed warnings when Rowv and
+ Colv were specified as dendrograms
+
+2006-03-10 17:24 warnes
+
+ * tests/heatmap2Test.R: Remove code that added a local path
+
+2006-03-09 22:53 nj7w
+
+ * tests/heatmap2Test.R, tests/heatmap2Test.Rout.save: Added the
+ correct library path where gplots is installed locally and
+ corresponding .save file
+
+2006-03-09 22:40 nj7w
+
+ * tests/heatmap2Test.R: Updated the tests file
+
+2006-03-09 22:39 nj7w
+
+ * R/heatmap.2.R: Removed the condition Colv != Rowv as it has
+ already been taken care of
+
+2006-03-09 22:17 nj7w
+
+ * rtPCR.rda: Deleted rtPCR.rda from the main directory
+
+2006-03-09 22:09 nj7w
+
+ * ChangeLog: Added ChangeLog
+
+2006-03-07 18:18 nj7w
+
+ * DESCRIPTION, NEWS: Updated ChangeLog and NEWS
+
+2006-03-07 18:10 nj7w
+
+ * tests, tests/heatmap2Test.R, tests/heatmap2Test.Rout.save: Added
+ the tests and fixed corrupted files
+
2006-03-07 16:22 nj7w
- * trunk/gplots/data/rtPCR.rda: Replaced the corrupted rtPCR.rda
- file in data directory
+ * data/rtPCR.rda: Replaced the corrupted rtPCR.rda file in data
+ directory
2006-03-07 16:14 nj7w
- * trunk/gplots/tests: Removed the corrputed tests directory
+ * tests: Removed the corrputed tests directory
2006-03-07 16:12 nj7w
- * trunk/gplots/data/rtPCR.rda, trunk/gplots/rtPCR.rda: Replaced
- the corrupted rtPCR.rda file in data directory
+ * data/rtPCR.rda, rtPCR.rda: Replaced the corrupted rtPCR.rda file
+ in data directory
2006-03-03 21:03 nj7w
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd:
- Updated the code and man page to make sure the Rowv and Colv
- values are properly handled
+ * R/heatmap.2.R, man/heatmap.2.Rd: Updated the code and man page to
+ make sure the Rowv and Colv values are properly handled
2006-03-02 21:43 warnes
- * trunk/gplots/R/balloonplot.R: Adjust row total placement to
- adjust for width of the totals
+ * R/balloonplot.R: Adjust row total placement to adjust for width
+ of the totals
2006-03-02 21:26 warnes
- * trunk/gplots/DESCRIPTION, trunk/gplots/R/balloonplot.R,
- trunk/gplots/man/1: Row totals in ballonplot were in reverse
- order. Fixed.
+ * DESCRIPTION, R/balloonplot.R, man/1: Row totals in ballonplot
+ were in reverse order. Fixed.
2006-02-23 22:00 nj7w
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/tests/heatmap2Test.R:
- Add ability to scale the color key using the new 'keysize'
- argument.
+ * R/heatmap.2.R, tests/heatmap2Test.R: Add ability to scale the
+ color key using the new 'keysize' argument.
2006-02-23 21:34 nj7w
- * trunk/gplots/tests, trunk/gplots/tests/heatmap2Test.R,
- trunk/gplots/tests/heatmap2Test.Rout.save: Add tests for
- heatmap.2
+ * tests, tests/heatmap2Test.R, tests/heatmap2Test.Rout.save: Add
+ tests for heatmap.2
2006-02-23 21:25 nj7w
- * trunk/gplots/inst/doc/Figure1.eps,
- trunk/gplots/inst/doc/Table.eps, trunk/gplots/inst/doc/bka.bst,
- trunk/gplots/inst/doc/heatmap2.R,
- trunk/gplots/inst/doc/heatmap2.tex,
- trunk/gplots/inst/doc/regression_rank_image.Rda,
- trunk/gplots/inst/doc/regression_rank_image_II.Rda: Move heatmap
- and ballonplot paper source materials to their respective cvs
- modules
+ * inst/doc/Figure1.eps, inst/doc/Table.eps, inst/doc/bka.bst,
+ inst/doc/heatmap2.R, inst/doc/heatmap2.tex,
+ inst/doc/regression_rank_image.Rda,
+ inst/doc/regression_rank_image_II.Rda: Move heatmap and
+ ballonplot paper source materials to their respective cvs modules
2006-02-23 21:20 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.R,
- trunk/gplots/inst/doc/BalloonPlot.tex,
- trunk/gplots/inst/doc/Figure1.pdf,
- trunk/gplots/inst/doc/Figure2.pdf,
- trunk/gplots/inst/doc/Figure3.pdf,
- trunk/gplots/inst/doc/Figure4.pdf,
- trunk/gplots/inst/doc/Rnews.sty,
- trunk/gplots/inst/doc/SurvivedPop.pdf,
- trunk/gplots/inst/doc/SurvivedPopWhite.pdf,
- trunk/gplots/inst/doc/SurvivedProp.pdf,
- trunk/gplots/inst/doc/TotalPop.pdf: Moved balloonplot paper
- materials to BallonPlotPaper cvs module
+ * inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex,
+ inst/doc/Figure1.pdf, inst/doc/Figure2.pdf, inst/doc/Figure3.pdf,
+ inst/doc/Figure4.pdf, inst/doc/Rnews.sty,
+ inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
+ inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Moved
+ balloonplot paper materials to BallonPlotPaper cvs module
2006-02-23 21:18 nj7w
- * trunk/gplots/inst/doc/colSeparator.pdf,
- trunk/gplots/inst/doc/logData.pdf,
- trunk/gplots/inst/doc/logDataColDendrogram.pdf,
- trunk/gplots/inst/doc/logDataColOrd.pdf,
- trunk/gplots/inst/doc/logDataColOrdNo.pdf,
- trunk/gplots/inst/doc/logDataRowDendrogram.pdf,
- trunk/gplots/inst/doc/origScale.pdf,
- trunk/gplots/inst/doc/rowSeparator.pdf,
- trunk/gplots/inst/doc/scaled.pdf: Remove heatmap paper files and
- move them to the HeatmapPaper cvs module.
+ * inst/doc/colSeparator.pdf, inst/doc/logData.pdf,
+ inst/doc/logDataColDendrogram.pdf, inst/doc/logDataColOrd.pdf,
+ inst/doc/logDataColOrdNo.pdf, inst/doc/logDataRowDendrogram.pdf,
+ inst/doc/origScale.pdf, inst/doc/rowSeparator.pdf,
+ inst/doc/scaled.pdf: Remove heatmap paper files and move them to
+ the HeatmapPaper cvs module.
2006-02-23 19:57 nj7w
- * trunk/gplots/inst/doc/colSeparator.pdf,
- trunk/gplots/inst/doc/logData.pdf,
- trunk/gplots/inst/doc/logDataColDendrogram.pdf,
- trunk/gplots/inst/doc/logDataColOrd.pdf,
- trunk/gplots/inst/doc/logDataColOrdNo.pdf,
- trunk/gplots/inst/doc/logDataRowDendrogram.pdf,
- trunk/gplots/inst/doc/origScale.pdf,
- trunk/gplots/inst/doc/rowSeparator.pdf,
- trunk/gplots/inst/doc/scaled.pdf: Added figures for heatmap2
- paper
+ * inst/doc/colSeparator.pdf, inst/doc/logData.pdf,
+ inst/doc/logDataColDendrogram.pdf, inst/doc/logDataColOrd.pdf,
+ inst/doc/logDataColOrdNo.pdf, inst/doc/logDataRowDendrogram.pdf,
+ inst/doc/origScale.pdf, inst/doc/rowSeparator.pdf,
+ inst/doc/scaled.pdf: Added figures for heatmap2 paper
2006-02-23 19:54 nj7w
- * trunk/gplots/inst/doc/regression_rank_image.Rda,
- trunk/gplots/inst/doc/regression_rank_image_II.Rda: Added the
- .Rda files for the heatmap2 paper
+ * inst/doc/regression_rank_image.Rda,
+ inst/doc/regression_rank_image_II.Rda: Added the .Rda files for
+ the heatmap2 paper
2006-02-23 19:52 nj7w
- * trunk/gplots/inst/doc/heatmap2.tex: Added the source - (tex
- file) of the heatmap paper
+ * inst/doc/heatmap2.tex: Added the source - (tex file) of the
+ heatmap paper
2006-02-23 19:51 nj7w
- * trunk/gplots/inst/doc/heatmap2.R: Added the code for the figures
- of heatmap paper
+ * inst/doc/heatmap2.R: Added the code for the figures of heatmap
+ paper
2006-02-21 22:19 nj7w
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd: Minor
- updates to heatmap.2 - fixed Rowv, Colv and dendrogram
- behaviour. Now Rowv=NULL or FALSE both imply no dendrogram
- computation.
+ * R/heatmap.2.R, man/heatmap.2.Rd: Minor updates to heatmap.2 -
+ fixed Rowv, Colv and dendrogram behaviour. Now Rowv=NULL or FALSE
+ both imply no dendrogram computation.
2006-01-12 23:10 warnes
- * trunk/gplots/inst/doc/BalloonPlot.R,
- trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex,
- trunk/gplots/inst/doc/Figure1.pdf,
- trunk/gplots/inst/doc/Figure2.pdf,
- trunk/gplots/inst/doc/Figure3.pdf,
- trunk/gplots/inst/doc/Figure4.pdf: more updates
+ * inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.pdf,
+ inst/doc/BalloonPlot.tex, inst/doc/Figure1.pdf,
+ inst/doc/Figure2.pdf, inst/doc/Figure3.pdf, inst/doc/Figure4.pdf:
+ more updates
2006-01-12 23:01 warnes
- * trunk/gplots/inst/doc/bka.bst: Add Biometrica bibliography style
- file
+ * inst/doc/bka.bst: Add Biometrica bibliography style file
2006-01-12 22:34 warnes
- * trunk/gplots/inst/doc/BalloonPlot.tex: A little more.
+ * inst/doc/BalloonPlot.tex: A little more.
2006-01-12 22:32 warnes
- * trunk/gplots/inst/doc/BalloonPlot.tex: Updates to respond to
- referee.
+ * inst/doc/BalloonPlot.tex: Updates to respond to referee.
2006-01-12 19:59 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.tex: Added references
+ * inst/doc/BalloonPlot.tex: Added references
2005-12-13 17:01 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.tex: Fixed Nitin's company name
+ * inst/doc/BalloonPlot.tex: Fixed Nitin's company name
2005-12-13 16:18 nj7w
- * trunk/gplots/ChangeLog, trunk/gplots/NEWS, trunk/gtools/NEWS:
- Updated NEWS and removed ChangeLog
+ * ChangeLog, NEWS, trunk/gtools/NEWS: Updated NEWS and removed
+ ChangeLog
2005-12-12 22:20 nj7w
- * trunk/gplots/R/plotmeans.R: Fixed bug in plotmeans - based on
- Stefano Calza's suggestion
+ * R/plotmeans.R: Fixed bug in plotmeans - based on Stefano Calza's
+ suggestion
2005-12-07 18:52 nj7w
- * trunk/gplots/DESCRIPTION: Updated version number
+ * DESCRIPTION: Updated version number
2005-12-07 18:50 nj7w
- * trunk/gplots/NAMESPACE, trunk/gplots/R/plot.lm.R,
- trunk/gplots/man/plot.lm2.Rd: Added plot.lm
+ * NAMESPACE, R/plot.lm.R, man/plot.lm2.Rd: Added plot.lm
2005-12-07 18:48 nj7w
- * trunk/gplots/man/barplot2.Rd: Changed the default grey colors to
- heat colors, if height is matrix
- * trunk/gplots/R/barplot2.R: Changed the default greay colors to
- heat colors, if height is matrix
+ * man/barplot2.Rd: Changed the default grey colors to heat colors,
+ if height is matrix
+2005-12-07 18:48 nj7w
+
+ * R/barplot2.R: Changed the default greay colors to heat colors, if
+ height is matrix
+
2005-12-06 22:41 nj7w
- * trunk/gplots/man/barplot2.Rd: Fixed minor error in documentation
- of barplot2
+ * man/barplot2.Rd: Fixed minor error in documentation of barplot2
2005-12-02 21:11 warnes
- * trunk/gplots/R/plot.lm.R: Remove .Alias calls, since .Alias is
- defunct.
+ * R/plot.lm.R: Remove .Alias calls, since .Alias is defunct.
2005-12-01 16:54 nj7w
* trunk/gmodels/man/ci.Rd, trunk/gmodels/man/coefFrame.Rd,
trunk/gmodels/man/estimable.Rd,
trunk/gmodels/man/fit.contrast.Rd,
- trunk/gmodels/man/make.contrasts.Rd,
- trunk/gplots/man/balloonplot.Rd, trunk/gplots/man/bandplot.Rd,
- trunk/gplots/man/boxplot.n.Rd, trunk/gplots/man/colorpanel.Rd,
- trunk/gplots/man/overplot.Rd, trunk/gplots/man/plotmeans.Rd,
- trunk/gplots/man/textplot.Rd, trunk/gplots/man/wapply.Rd,
- trunk/gtools/man/combinations.Rd,
+ trunk/gmodels/man/make.contrasts.Rd, man/balloonplot.Rd,
+ man/bandplot.Rd, man/boxplot.n.Rd, man/colorpanel.Rd,
+ man/overplot.Rd, man/plotmeans.Rd, man/textplot.Rd,
+ man/wapply.Rd, trunk/gtools/man/combinations.Rd,
trunk/gtools/man/foldchange.Rd, trunk/gtools/man/invalid.Rd,
trunk/gtools/man/logit.Rd, trunk/gtools/man/mixedsort.Rd,
trunk/gtools/man/oddeven.Rd, trunk/gtools/man/quantcut.Rd,
@@ -202,187 +264,179 @@
2005-11-23 22:05 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.R,
- trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex,
- trunk/gplots/inst/doc/Figure2.pdf: Updated Figure 2 colors
+ * inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.pdf,
+ inst/doc/BalloonPlot.tex, inst/doc/Figure2.pdf: Updated Figure 2
+ colors
2005-11-18 20:40 warnes
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/Figure1.pdf,
- trunk/gplots/inst/doc/Figure2.pdf,
- trunk/gplots/inst/doc/Figure3.pdf,
- trunk/gplots/inst/doc/Figure4.pdf: Latest version of the pdf
- files
+ * inst/doc/BalloonPlot.pdf, inst/doc/Figure1.pdf,
+ inst/doc/Figure2.pdf, inst/doc/Figure3.pdf, inst/doc/Figure4.pdf:
+ Latest version of the pdf files
2005-11-18 20:37 warnes
- * trunk/gplots/inst/doc/BalloonPlot.tex: Nitin works for the
- Cambrige Group, not Pfizer.
+ * inst/doc/BalloonPlot.tex: Nitin works for the Cambrige Group, not
+ Pfizer.
2005-11-18 20:34 warnes
- * trunk/gplots/inst/doc/BalloonPlot.tex: Minor text rewording.
+ * inst/doc/BalloonPlot.tex: Minor text rewording.
2005-11-18 20:31 warnes
- * trunk/gplots/inst/doc/BalloonPlot.R,
- trunk/gplots/inst/doc/BalloonPlot.tex: More edits.
+ * inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex: More edits.
2005-11-18 19:50 warnes
- * trunk/gplots/R/balloonplot.R: Recent changes to align row totals
- with the overall total broke how
+ * R/balloonplot.R: Recent changes to align row totals with the
+ overall total broke how
the marginal cumulative fractions were displayed. This patch
fixes
the problem.
2005-11-18 01:17 warnes
- * trunk/gplots/DESCRIPTION, trunk/gplots/R/balloonplot.R,
- trunk/gplots/R/plot.lm.R, trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/man/balloonplot.Rd: - Update documentation for
- balloonplot to match the latest code.
+ * DESCRIPTION, R/balloonplot.R, R/plot.lm.R,
+ inst/doc/BalloonPlot.pdf, man/balloonplot.Rd: - Update
+ documentation for balloonplot to match the latest code.
- Correct spelling of 'show.zeroes' to 'show.zeros'
2005-11-18 00:16 warnes
- * trunk/gplots/R/colorpanel.R: More changes: colorpanel now allows
- only 2 colors to be specified if
+ * R/colorpanel.R: More changes: colorpanel now allows only 2 colors
+ to be specified if
no 'middle' color is desired.
2005-11-17 22:08 warnes
- * trunk/gplots/R/balloonplot.R: Allow user to control removal of
- duplicate entries in balloonplot.
+ * R/balloonplot.R: Allow user to control removal of duplicate
+ entries in balloonplot.
2005-11-17 22:06 warnes
- * trunk/gplots/R/colorpanel.R, trunk/gplots/man/colorpanel.Rd:
- Extend colorpanel to handle just two-colors in addition to three.
+ * R/colorpanel.R, man/colorpanel.Rd: Extend colorpanel to handle
+ just two-colors in addition to three.
2005-11-09 22:39 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.pdf: Updated the pdf file
+ * inst/doc/BalloonPlot.pdf: Updated the pdf file
2005-11-09 22:38 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.R,
- trunk/gplots/inst/doc/BalloonPlot.tex: Updated the changes
+ * inst/doc/BalloonPlot.R, inst/doc/BalloonPlot.tex: Updated the
+ changes
2005-11-09 22:29 nj7w
- * trunk/gplots/inst/doc/Figure4.pdf: Modified figure 4
- * trunk/gplots/inst/doc/BalloonPlot.R: Updated code
+ * inst/doc/Figure4.pdf: Modified figure 4
+2005-11-09 22:29 nj7w
+
+ * inst/doc/BalloonPlot.R: Updated code
+
2005-11-09 22:20 nj7w
- * trunk/gplots/inst/doc/Figure3.pdf: Modified figure 3
- * trunk/gplots/inst/doc/Figure2.pdf: Modified figure 2
+ * inst/doc/Figure3.pdf: Modified figure 3
+2005-11-09 22:20 nj7w
+
+ * inst/doc/Figure2.pdf: Modified figure 2
+
2005-11-09 22:19 nj7w
- * trunk/gplots/inst/doc/Figure1.pdf: Modified figure 1
+ * inst/doc/Figure1.pdf: Modified figure 1
2005-11-08 16:19 nj7w
- * trunk/gplots/man/plotCI.Rd: Updated Greg's email
+ * man/plotCI.Rd: Updated Greg's email
2005-11-07 16:58 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex: Minor modifications to
- fit the code properly on pdf
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Minor
+ modifications to fit the code properly on pdf
2005-11-07 14:22 warnes
- * trunk/gplots/inst/doc/BalloonPlot.R: Add R code that generates
- plots
+ * inst/doc/BalloonPlot.R: Add R code that generates plots
2005-11-07 14:18 warnes
- * trunk/gplots/inst/doc/Figure2.pdf,
- trunk/gplots/inst/doc/Figure3.pdf,
- trunk/gplots/inst/doc/Figure4.pdf: Add figures to CVS
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex,
- trunk/gplots/inst/doc/Figure1.pdf: Text changes
+ * inst/doc/Figure2.pdf, inst/doc/Figure3.pdf, inst/doc/Figure4.pdf:
+ Add figures to CVS
+2005-11-07 14:18 warnes
+
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex,
+ inst/doc/Figure1.pdf: Text changes
+
2005-11-04 21:48 warnes
- * trunk/gplots/R/balloonplot.R: Fix some alignment issues.
+ * R/balloonplot.R: Fix some alignment issues.
2005-11-04 19:05 warnes
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/Table.pdf: Remove Table.pdf since it is no
- longer needed
+ * inst/doc/BalloonPlot.pdf, inst/doc/Table.pdf: Remove Table.pdf
+ since it is no longer needed
2005-11-04 19:04 warnes
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex,
- trunk/gplots/inst/doc/Figure1.pdf: Nitin's Changes
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex,
+ inst/doc/Figure1.pdf: Nitin's Changes
2005-11-04 19:00 warnes
- * trunk/gplots/inst/doc/SurvivedPop.pdf,
- trunk/gplots/inst/doc/SurvivedPopWhite.pdf,
- trunk/gplots/inst/doc/SurvivedProp.pdf,
- trunk/gplots/inst/doc/TotalPop.pdf: Add figure plots
+ * inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
+ inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Add figure
+ plots
2005-11-04 18:59 warnes
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex: Fix paths
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Fix paths
2005-10-20 18:36 nj7w
- * trunk/gplots/inst/doc/Figure1.eps,
- trunk/gplots/inst/doc/Table.eps: added the eps version of figures
+ * inst/doc/Figure1.eps, inst/doc/Table.eps: added the eps version
+ of figures
2005-10-20 18:35 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.pdf: Updated BallonPlot.pdf
+ * inst/doc/BalloonPlot.pdf: Updated BallonPlot.pdf
2005-10-20 18:34 nj7w
- * trunk/gplots/inst/doc/SurvivedPop.pdf,
- trunk/gplots/inst/doc/SurvivedPopWhite.pdf,
- trunk/gplots/inst/doc/SurvivedProp.pdf,
- trunk/gplots/inst/doc/TotalPop.pdf: Removed Old Figure
+ * inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
+ inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Removed Old
+ Figure
2005-10-20 18:31 nj7w
- * trunk/gplots/inst/doc/Figure1.pdf,
- trunk/gplots/inst/doc/Table.pdf: Added the new figure - for
- total popluation - Balloonplot
+ * inst/doc/Figure1.pdf, inst/doc/Table.pdf: Added the new figure -
+ for total popluation - Balloonplot
2005-10-20 18:29 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.tex: Modified the BallonPlot
- article
+ * inst/doc/BalloonPlot.tex: Modified the BallonPlot article
2005-10-20 14:12 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.tex: Added references
+ * inst/doc/BalloonPlot.tex: Added references
2005-10-19 16:57 arnima
- * trunk/gplots/man/rich.color.Rd: The last example now displays
- the correct heat.colors.
+ * man/rich.color.Rd: The last example now displays the correct
+ heat.colors.
Default 'palette' argument is now a single string, not a vector.
2005-10-19 16:56 arnima
- * trunk/gplots/R/rich.color.R: Default 'palette' argument is now a
- single string, not a vector.
+ * R/rich.color.R: Default 'palette' argument is now a single
+ string, not a vector.
2005-10-14 19:13 warnes
- * trunk/gplots/DESCRIPTION, trunk/gplots/R/balloonplot.R,
- trunk/gplots/man/balloonplot.Rd: Formatting fixes:
+ * DESCRIPTION, R/balloonplot.R, man/balloonplot.Rd: 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
@@ -390,54 +444,50 @@
2005-10-13 20:00 warnes
- * trunk/gplots/man/balloonplot.Rd: Add example using Titanic data
- that exercises the multi-factor
+ * man/balloonplot.Rd: Add example using Titanic data that exercises
+ the multi-factor
display.
2005-10-11 21:20 warnes
- * trunk/gplots/R/balloonplot.R: Initial changes to allow multiple
- x and y factor variables. Yet to
+ * R/balloonplot.R: 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 19:39 warnes
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex: more minor fixes
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: more minor
+ fixes
2005-10-04 19:29 warnes
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex: fix spacing
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: fix spacing
2005-10-04 19:08 warnes
- * trunk/gplots/inst/doc/Rnews.sty: Inlcude Rnews.sty
+ * inst/doc/Rnews.sty: Inlcude Rnews.sty
2005-10-04 19:07 warnes
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex: Some textual edits.
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Some textual
+ edits.
2005-10-03 16:23 nj7w
- * trunk/gplots/inst/doc/SurvivedPop.pdf,
- trunk/gplots/inst/doc/SurvivedPopWhite.pdf,
- trunk/gplots/inst/doc/SurvivedProp.pdf,
- trunk/gplots/inst/doc/TotalPop.pdf: Added figures for the R-News
- Article
+ * inst/doc/SurvivedPop.pdf, inst/doc/SurvivedPopWhite.pdf,
+ inst/doc/SurvivedProp.pdf, inst/doc/TotalPop.pdf: Added figures
+ for the R-News Article
2005-09-29 21:02 nj7w
- * trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex: Updated the documentation
- - added the name of the person who asked the question
+ * inst/doc/BalloonPlot.pdf, inst/doc/BalloonPlot.tex: Updated the
+ documentation - added the name of the person who asked the
+ question
2005-09-29 20:29 nj7w
- * trunk/gplots/inst, trunk/gplots/inst/doc,
- trunk/gplots/inst/doc/BalloonPlot.pdf,
- trunk/gplots/inst/doc/BalloonPlot.tex: Added R-news article
+ * inst, inst/doc, inst/doc/BalloonPlot.pdf,
+ inst/doc/BalloonPlot.tex: Added R-news article
2005-09-12 15:44 nj7w
@@ -446,47 +496,47 @@
trunk/gdata/man/nobs.Rd, trunk/gdata/man/read.xls.Rd,
trunk/gdata/man/rename.vars.Rd, trunk/gdata/man/trim.Rd,
trunk/gdata/man/unmatrix.Rd, trunk/gmodels/man/fast.prcomp.Rd,
- trunk/gmodels/man/glh.test.Rd, trunk/gplots/man/hist2d.Rd,
- trunk/gplots/man/ooplot.Rd, trunk/gplots/man/residplot.Rd,
- trunk/gplots/man/sinkplot.Rd, trunk/gplots/man/smartlegend.Rd,
- trunk/gplots/man/space.Rd, trunk/gtools/man/assert.Rd,
+ trunk/gmodels/man/glh.test.Rd, man/hist2d.Rd, man/ooplot.Rd,
+ man/residplot.Rd, man/sinkplot.Rd, man/smartlegend.Rd,
+ man/space.Rd, trunk/gtools/man/assert.Rd,
trunk/gtools/man/dirichlet.Rd, trunk/gtools/man/permute.Rd,
trunk/gtools/man/scat.Rd: Updated Greg's email
2005-09-12 14:45 nj7w
- * trunk/gplots/R/balloonplot.R: Updated version of balloonplot -
- by Romain Francois <fra...@fr...>
+ * R/balloonplot.R: Updated version of balloonplot - by Romain
+ Francois <fra...@fr...>
2005-09-09 20:34 nj7w
- * trunk/gplots/ChangeLog, trunk/gplots/DESCRIPTION: Updated the
- version and ChangeLog
+ * ChangeLog, DESCRIPTION: Updated the version and ChangeLog
2005-09-09 20:32 nj7w
- * trunk/gplots/R/balloonplot.R, trunk/gplots/man/balloonplot.Rd:
- Changes in ballon plot based on Romain Francois
- (fra...@fr...) suggestions
+ * R/balloonplot.R, man/balloonplot.Rd: Changes in ballon plot based
+ on Romain Francois (fra...@fr...) suggestions
2005-09-06 21:41 nj7w
- * trunk/gplots/DESCRIPTION: Updated package dependencies
- * trunk/gplots/NEWS: Added NEWS
+ * DESCRIPTION: Updated package dependencies
+2005-09-06 21:41 nj7w
+
+ * NEWS: Added NEWS
+
2005-09-02 23:10 nj7w
- * trunk/gmodels/ChangeLog, trunk/gplots/ChangeLog: Added ChangeLog
+ * trunk/gmodels/ChangeLog, ChangeLog: Added ChangeLog
2005-08-31 16:28 nj7w
- * trunk/gdata/DESCRIPTION, trunk/gmodels/DESCRIPTION,
- trunk/gplots/DESCRIPTION: Added DESCRIPTION file
+ * trunk/gdata/DESCRIPTION, trunk/gmodels/DESCRIPTION, DESCRIPTION:
+ Added DESCRIPTION file
2005-08-31 16:27 nj7w
* trunk/gdata/DESCRIPTION.in, trunk/gmodels/DESCRIPTION.in,
- trunk/gplots/DESCRIPTION.in: removed DESCRIPTION.in
+ DESCRIPTION.in: removed DESCRIPTION.in
2005-06-09 14:20 nj7w
@@ -498,8 +548,7 @@
trunk/gdata/R/matchcols.R, trunk/gdata/R/nobs.R,
trunk/gdata/R/read.xls.R, trunk/gdata/R/rename.vars.R,
trunk/gdata/R/reorder.R, trunk/gdata/R/trim.R,
- trunk/gdata/R/unmatrix.R,
- trunk/gdata/inst/perl/IO/AtomicFile.pm,
+ trunk/gdata/R/unmatrix.R, trunk/gdata/inst/perl/IO/AtomicFile.pm,
trunk/gdata/inst/perl/IO/InnerFile.pm,
trunk/gdata/inst/perl/IO/Lines.pm,
trunk/gdata/inst/perl/IO/Scalar.pm,
@@ -518,24 +567,15 @@
trunk/gmodels/man/CrossTable.Rd, trunk/gmodels/man/ci.Rd,
trunk/gmodels/man/coefFrame.Rd, trunk/gmodels/man/estimable.Rd,
trunk/gmodels/man/fast.prcomp.Rd,
- trunk/gmodels/man/fit.contrast.Rd,
- trunk/gmodels/man/glh.test.Rd,
- trunk/gmodels/man/make.contrasts.Rd,
- trunk/gplots/R/balloonplot.R, trunk/gplots/R/bandplot.R,
- trunk/gplots/R/boxplot.n.R, trunk/gplots/R/colorpanel.R,
- trunk/gplots/R/heatmap.2.R, trunk/gplots/R/hist2d.R,
- trunk/gplots/R/lowess.R, trunk/gplots/R/ooplot.R,
- trunk/gplots/R/overplot.R, trunk/gplots/R/plotCI.R,
- trunk/gplots/R/plotmeans.R, trunk/gplots/R/qqnorm.aov.R,
- trunk/gplots/R/residplot.R, trunk/gplots/R/rich.color.R,
- trunk/gplots/R/sinkplot.R, trunk/gplots/R/smartlegend.R,
- trunk/gplots/R/space.R, trunk/gplots/R/textplot.R,
- trunk/gplots/R/wapply.R, trunk/gplots/man/1,
- trunk/gplots/man/bandplot.Rd, trunk/gplots/man/barplot2.Rd,
- trunk/gplots/man/boxplot.n.Rd, trunk/gplots/man/hist2d.Rd,
- trunk/gplots/man/lowess.Rd, trunk/gplots/man/plotCI.Rd,
- trunk/gplots/man/plotmeans.Rd, trunk/gplots/man/residplot.Rd,
- trunk/gplots/man/space.Rd, trunk/gplots/man/wapply.Rd,
+ trunk/gmodels/man/fit.contrast.Rd, trunk/gmodels/man/glh.test.Rd,
+ trunk/gmodels/man/make.contrasts.Rd, R/balloonplot.R,
+ R/bandplot.R, R/boxplot.n.R, R/colorpanel.R, R/heatmap.2.R,
+ R/hist2d.R, R/lowess.R, R/ooplot.R, R/overplot.R, R/plotCI.R,
+ R/plotmeans.R, R/qqnorm.aov.R, R/residplot.R, R/rich.color.R,
+ R/sinkplot.R, R/smartlegend.R, R/space.R, R/textplot.R,
+ R/wapply.R, man/1, man/bandplot.Rd, man/barplot2.Rd,
+ man/boxplot.n.Rd, man/hist2d.Rd, man/lowess.Rd, man/plotCI.Rd,
+ man/plotmeans.Rd, man/residplot.Rd, man/space.Rd, man/wapply.Rd,
trunk/gtools/R/RSCompat.S, trunk/gtools/R/combinations.R,
trunk/gtools/R/dirichlet.R, trunk/gtools/R/foldchange.R,
trunk/gtools/R/invalid.R, trunk/gtools/R/logit.R,
@@ -553,22 +593,21 @@
2005-06-09 14:15 nj7w
- * trunk/gplots/R/barplot2.R: Changes based on Marc Schwartz's
- suggestions to handel 0's and NA's appropriately.
+ * R/barplot2.R: Changes based on Marc Schwartz's suggestions to
+ handel 0's and NA's appropriately.
2005-05-13 18:59 nj7w
* trunk/gdata/R/read.xls.R, trunk/gmodels/man/CrossTable.Rd,
- trunk/gplots/man/heatmap.2.Rd: 1) Using dQuote.ascii function in
- read.xls as the new version of dQuote doesn't work proprly with
- UTF-8 locale.
+ man/heatmap.2.Rd: 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 14:23 warnes
- * trunk/gplots/R/overplot.R: Explicitly reference package
- containing lowess.formula in
+ * R/overplot.R: Explicitly reference package containing
+ lowess.formula in
panel.overplot(). This should fix the error reported by Troels
Ring
<tr...@gv...>.
@@ -577,57 +616,55 @@
* trunk/gdata/NAMESPACE, trunk/gdata/man/elem.Rd,
trunk/gdata/man/env.Rd, trunk/gdata/man/ll.Rd,
- trunk/gdata/man/read.xls.Rd, trunk/gplots/R/heatmap.2.R,
- trunk/gplots/man/heatmap.2.Rd, trunk/gplots/man/rich.color.Rd,
- trunk/gplots/man/sinkplot.Rd, trunk/gplots/man/textplot.Rd: ***
- empty log message ***
+ trunk/gdata/man/read.xls.Rd, R/heatmap.2.R, man/heatmap.2.Rd,
+ man/rich.color.Rd, man/sinkplot.Rd, man/textplot.Rd: *** empty
+ log message ***
2005-02-25 23:22 warnes
* trunk/gdata/R/elem.R, trunk/gdata/R/env.R, trunk/gdata/R/ll.R,
trunk/gdata/man/Args.Rd, trunk/gdata/man/env.Rd,
- trunk/gdata/man/ll.Rd, trunk/gplots/man/rich.color.Rd: Integrate
- changes submitted by Arni Magnusson
+ trunk/gdata/man/ll.Rd, man/rich.color.Rd: Integrate changes
+ submitted by Arni Magnusson
2005-02-25 22:31 warnes
- * trunk/gplots/NAMESPACE: Add dependency imports from 'stats'
- package.
+ * NAMESPACE: Add dependency imports from 'stats' package.
2005-02-22 21:01 warnes
- * trunk/gplots/R/bandplot.R: Fix problem in passing graphical
- parameters (xlim,etc).@
+ * R/bandplot.R: Fix problem in passing graphical parameters
+ (xlim,etc).@
2005-02-08 16:41 warnes
- * trunk/gplots/DESCRIPTION.in: Improve package title.
+ * DESCRIPTION.in: Improve package title.
2005-02-08 16:40 warnes
- * trunk/gplots/R/heatmap.2.R: Ignore missing values when computing
- symmetric range.
+ * R/heatmap.2.R: Ignore missing values when computing symmetric
+ range.
2005-02-02 19:25 warnes
- * trunk/gplots/man/plotmeans.Rd: Add more extensive example.
+ * man/plotmeans.Rd: Add more extensive example.
2005-01-14 19:05 warnes
- * trunk/gplots/R/textplot.R: Code can be simplified because R now
- supports selecting a fixed width font.
+ * R/textplot.R: Code can be simplified because R now supports
+ selecting a fixed width font.
2005-01-12 20:50 warnes
* trunk/gdata/DESCRIPTION.in, trunk/gmodels/DESCRIPTION.in,
- trunk/gplots/DESCRIPTION.in, trunk/gtools/DESCRIPTION.in: Add
- dependency on R 1.9.0+ to prevent poeple from installing on old
+ DESCRIPTION.in, trunk/gtools/DESCRIPTION.in: 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 01:06 warnes
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd: 1.
- Add new parameters for controlling color key:
+ * R/heatmap.2.R, man/heatmap.2.Rd: 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
@@ -640,8 +677,7 @@
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
+ 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
@@ -649,8 +685,8 @@
2004-11-03 19:43 warnes
- * trunk/gplots/R/heatmap.2.R: Fix bugs in layout of cell notes.
- They were being plotted top down
+ * R/heatmap.2.R: 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.
@@ -659,18 +695,19 @@
* trunk/gdata/DESCRIPTION, trunk/gdata/DESCRIPTION.in,
trunk/gdata/NAMESPACE, trunk/gdata/man/.Rhistory,
trunk/gmodels/DESCRIPTION, trunk/gmodels/DESCRIPTION.in,
- trunk/gplots/DESCRIPTION, trunk/gplots/DESCRIPTION.in,
- trunk/gplots/man/sinkplot.Rd, trunk/gplots/man/textplot.Rd,
+ DESCRIPTION, DESCRIPTION.in, man/sinkplot.Rd, man/textplot.Rd,
trunk/gregmisc/.Rhistory, trunk/gregmisc/DESCRIPTION,
trunk/gtools/DESCRIPTION, trunk/gtools/DESCRIPTION.in,
trunk/gtools/man/running.Rd: Updated to pass R CMD check.
2004-09-03 22:50 warneg
- * trunk/gplots/man/textplot.Rd: Provide explicit package for call
- to nobs.
- * trunk/gplots/man/heatmap.2.Rd: Fix typos.
+ * man/textplot.Rd: Provide explicit package for call to nobs.
+2004-09-03 22:50 warneg
+
+ * man/heatmap.2.Rd: Fix typos.
+
2004-09-03 17:27 warneg
* trunk/gdata/DESCRIPTION, trunk/gdata/DESCRIPTION.in,
@@ -688,58 +725,49 @@
trunk/gmodels/R/fast.prcomp.R, trunk/gmodels/R/fit.contrast.R,
trunk/gmodels/R/glh.test.R, trunk/gmodels/R/make.contrasts.R,
trunk/gmodels/man/estimable.Rd,
- trunk/gmodels/man/fit.contrast.Rd,
- trunk/gmodels/man/glh.test.Rd,
- trunk/gmodels/man/make.contrasts.Rd, trunk/gplots/DESCRIPTION,
- trunk/gplots/NAMESPACE, trunk/gplots/R/balloonplot.R,
- trunk/gplots/R/bandplot.R, trunk/gplots/R/barplot2.R,
- trunk/gplots/R/boxplot.n.R, trunk/gplots/R/colorpanel.R,
- trunk/gplots/R/heatmap.2.R, trunk/gplots/R/hist2d.R,
- trunk/gplots/R/lowess.R, trunk/gplots/R/ooplot.R,
- trunk/gplots/R/overplot.R, trunk/gplots/R/plotCI.R,
- trunk/gplots/R/plotmeans.R, trunk/gplots/R/qqnorm.aov.R,
- trunk/gplots/R/residplot.R, trunk/gplots/R/rich.color.R,
- trunk/gplots/R/sinkplot.R, trunk/gplots/R/smartlegend.R,
- trunk/gplots/R/space.R, trunk/gplots/R/textplot.R,
- trunk/gplots/R/wapply.R, trunk/gtools/DESCRIPTION,
- trunk/gtools/NAMESPACE, trunk/gtools/R/dirichlet.R,
- trunk/gtools/R/foldchange.R, trunk/gtools/R/invalid.R,
- trunk/gtools/R/mixedsort.R, trunk/gtools/R/oddeven.R,
- trunk/gtools/R/permute.R, trunk/gtools/R/quantcut.R,
- trunk/gtools/R/running.R, trunk/gtools/man/running.Rd: initial
- bundle checkin
+ trunk/gmodels/man/fit.contrast.Rd, trunk/gmodels/man/glh.test.Rd,
+ trunk/gmodels/man/make.contrasts.Rd, DESCRIPTION, NAMESPACE,
+ R/balloonplot.R, R/bandplot.R, R/barplot2.R, R/boxplot.n.R,
+ R/colorpanel.R, R/heatmap.2.R, R/hist2d.R, R/lowess.R,
+ R/ooplot.R, R/overplot.R, R/plotCI.R, R/plotmeans.R,
+ R/qqnorm.aov.R, R/residplot.R, R/rich.color.R, R/sinkplot.R,
+ R/smartlegend.R, R/space.R, R/textplot.R, R/wapply.R,
+ trunk/gtools/DESCRIPTION, trunk/gtools/NAMESPACE,
+ trunk/gtools/R/dirichlet.R, trunk/gtools/R/foldchange.R,
+ trunk/gtools/R/invalid.R, trunk/gtools/R/mixedsort.R,
+ trunk/gtools/R/oddeven.R, trunk/gtools/R/permute.R,
+ trunk/gtools/R/quantcut.R, trunk/gtools/R/running.R,
+ trunk/gtools/man/running.Rd: initial bundle checkin
2004-09-02 17:14 warneg
* trunk/gdata/DESCRIPTION, trunk/gdata/DESCRIPTION.in,
trunk/gdata/NAMESPACE, trunk/gdata/man/.Rhistory,
trunk/gmodels/DESCRIPTION, trunk/gmodels/DESCRIPTION.in,
- trunk/gmodels/NAMESPACE, trunk/gplots/DESCRIPTION,
- trunk/gplots/DESCRIPTION.in, trunk/gplots/NAMESPACE,
- trunk/gplots/man/1, trunk/gplots/man/residplot.Rd,
- trunk/gregmisc/.Rhistory, trunk/gtools/DESCRIPTION,
- trunk/gtools/DESCRIPTION.in, trunk/gtools/NAMESPACE: Initial
- revision
+ trunk/gmodels/NAMESPACE, DESCRIPTION, DESCRIPTION.in, NAMESPACE,
+ man/1, man/residplot.Rd, trunk/gregmisc/.Rhistory,
+ trunk/gtools/DESCRIPTION, trunk/gtools/DESCRIPTION.in,
+ trunk/gtools/NAMESPACE: Initial revision
2004-07-29 14:49 warnes
- * trunk/gplots/R/plotCI.R, trunk/gplots/man/plotCI.Rd: Integrate
- changes from the version of plotCI maintained by Martin Maechler.
+ * R/plotCI.R, man/plotCI.Rd: Integrate changes from the version of
+ plotCI maintained by Martin Maechler.
2004-06-30 19:32 warnes
- * trunk/gplots/R/textplot.R: Remove commented-out code.
+ * R/textplot.R: Remove commented-out code.
2004-06-30 19:26 warnes
- * trunk/gplots/R/textplot.R: Fixed text size calculations
+ * R/textplot.R: Fixed text size calculations
2004-06-28 20:16 warnes
- * trunk/gplots/R/barplot2.R, trunk/gplots/man/barplot2.Rd: -
- 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
+ * R/barplot2.R, man/barplot2.Rd: - 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
@@ -748,234 +776,223 @@
2004-06-24 16:57 warnes
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd: Add
- ability to specify color of NA cells.
+ * R/heatmap.2.R, man/heatmap.2.Rd: Add ability to specify color of
+ NA cells.
2004-05-27 15:11 warnes
- * trunk/gplots/man/plotCI.Rd: Fix spelling error.
+ * man/plotCI.Rd: Fix spelling error.
2004-05-26 14:56 warnes
- * trunk/gplots/R/overplot.R: One more fix to get it right.
+ * R/overplot.R: One more fix to get it right.
2004-05-26 13:50 warnes
- * trunk/gplots/R/overplot.R: Use triple-colon operator ':::' to
- access plot.formula from the graphics package.
+ * R/overplot.R: Use triple-colon operator ':::' to access
+ plot.formula from the graphics package.
2004-05-26 13:19 warnes
- * trunk/gplots/man/rich.color.Rd: Replace 'F' by 'FALSE' to pass R
- CMD check.
+ * man/rich.color.Rd: Replace 'F' by 'FALSE' to pass R CMD check.
2004-05-25 18:32 warnes
- * trunk/gplots/R/overplot.R: Work around bug in R 1.9.X due to
- plot.formula() not having the same
+ * R/overplot.R: Work around bug in R 1.9.X due to plot.formula()
+ not having the same
arguments as plot().
2004-05-25 17:33 warnes
- * trunk/gplots/R/rich.color.R, trunk/gplots/man/rich.color.Rd: Add
- rich.colors() submitted by Arni Magnusson
- <arnima@u.washington.edu>.
+ * R/rich.color.R, man/rich.color.Rd: Add rich.colors() submitted by
+ Arni Magnusson <arnima@u.washington.edu>.
2004-05-25 02:58 warnes
- * trunk/gplots/R/ooplot.R, trunk/gplots/man/ooplot.Rd: ??
+ * R/ooplot.R, man/ooplot.Rd: ??
2004-05-24 23:43 warnes
- * trunk/gplots/R/plotCI.R, trunk/gplots/R/plotmeans.R: Modified to
- use invalid() to check arguments instead of missing().
+ * R/plotCI.R, R/plotmeans.R: Modified to use invalid() to check
+ arguments instead of missing().
This fixes some build errors under R-1.9.0-Patched.
2004-04-22 15:44 warnes
- * trunk/gplots/R/ooplot.R, trunk/gplots/man/ooplot.Rd: Integrate
- changes from Lodewijk Bonebakker <bon...@co...>
+ * R/ooplot.R, man/ooplot.Rd: Integrate changes from Lodewijk
+ Bonebakker <bon...@co...>
2004-04-13 13:42 warnes
- * trunk/gplots/R/space.R, trunk/gplots/man/space.Rd: Add ability
- to space points along 'y' direction.
+ * R/space.R, man/space.Rd: Add ability to space points along 'y'
+ direction.
2004-04-02 19:06 warnes
- * trunk/gplots/R/smartlegend.R: Fixed smartlegend() positioning
- when x and/or y axis are log-scale.
+ * R/smartlegend.R: Fixed smartlegend() positioning when x and/or y
+ axis are log-scale.
2004-03-30 19:04 warnes
- * trunk/gplots/R/textplot.R, trunk/gregmisc/DESCRIPTION: - Fix bug
- in textplot() reported by Wright, Kevin
- <kev...@pi...>.
+ * R/textplot.R, trunk/gregmisc/DESCRIPTION: - Fix bug in textplot()
+ reported by Wright, Kevin <kev...@pi...>.
2004-03-26 22:27 warnes
- * trunk/gplots/man/textplot.Rd: Update to match changes in
- textplot() code.
+ * man/textplot.Rd: Update to match changes in textplot() code.
2004-03-26 22:25 warnes
- * trunk/gplots/man/ooplot.Rd: Remove Windows EOL characters.
+ * man/ooplot.Rd: Remove Windows EOL characters.
2004-03-26 22:20 warnes
- * trunk/gplots/man/barplot2.Rd: - Remove some commented-out code.
+ * man/barplot2.Rd: - Remove some commented-out code.
- Remove cvs log tag.
2004-03-26 22:16 warnes
- * trunk/gplots/R/textplot.R: Misc changes.
+ * R/textplot.R: Misc changes.
2004-02-17 22:22 warnes
- * trunk/gplots/man/ooplot.Rd: Minor fix to ooplot documentation.
+ * man/ooplot.Rd: Minor fix to ooplot documentation.
2004-02-17 22:21 warnes
- * trunk/gplots/R/ooplot.R, trunk/gplots/man/ooplot.Rd: Integrate
- ooplot updates provided by Lodewijk Bonebakker
+ * R/ooplot.R, man/ooplot.Rd: Integrate ooplot updates provided by
+ Lodewijk Bonebakker
<bon...@co...>
2004-02-02 16:26 warnes
- * trunk/gplots/R/colorpanel.R, trunk/gplots/man/colorpanel.Rd: -
- Add colorpanel function, which generates a smoothly varying band
- of
+ * R/colorpanel.R, man/colorpanel.Rd: - Add colorpanel function,
+ which generates a smoothly varying band of
colors over a three color range (lo, mid, high).
2004-01-21 12:07 warnes
- * trunk/gplots/man/textplot.Rd: - Correct arguments to halign to
- match code.
+ * man/textplot.Rd: - Correct arguments to halign to match code.
2004-01-21 05:17 warnes
- * trunk/gplots/R/lowess.R: Track R 1.9.0's move of 'lowess' from
- the base package to the (new)
+ * R/lowess.R: Track R 1.9.0's move of 'lowess' from the base
+ package to the (new)
stats package.
2004-01-21 04:44 warnes
- * trunk/gplots/man/sinkplot.Rd: - Fix sinkplot() example by
- replacing 'T' with 'TRUE'.
+ * man/sinkplot.Rd: - Fix sinkplot() example by replacing 'T' with
+ 'TRUE'.
2004-01-21 04:42 warnes
- * trunk/gplots/man/ooplot.Rd: - Add some more details to the
- ooplot() documentation. The
+ * man/ooplot.Rd: - Add some more details to the ooplot()
+ documentation. The
documentation is *not* complete.
2004-01-21 04:31 warnes
- * trunk/gplots/R/textplot.R, trunk/gtools/R/capture.R: - Mark
- sprint() as depreciated.
+ * R/textplot.R, trunk/gtools/R/capture.R: - 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
+ displayed. Previouslt, character vectors were plotted on top of
+ each
other.
2004-01-19 23:43 warnes
- * trunk/gplots/R/sinkplot.R, trunk/gplots/man/sinkplot.Rd: New
- function sinkplot(), as requested on R-devel by Kevin Wright
+ * R/sinkplot.R, man/sinkplot.Rd: New function sinkplot(), as
+ requested on R-devel by Kevin Wright
<kw...@es...> in
https://www.stat.math.ethz.ch/pipermail/r-devel/2004-January/028483.html.
2004-01-15 05:14 warnes
- * trunk/gplots/R/ooplot.R, trunk/gplots/man/ooplot.Rd: Add initial
- code and docs for ooplot() function submitted by Lodewijk
+ * R/ooplot.R, man/ooplot.Rd: Add initial code and docs for ooplot()
+ function submitted by Lodewijk
Bonebakker <bon...@co...>.
2003-12-03 02:46 warnes
- * trunk/gdata/man/elem.Rd, trunk/gdata/man/ll.Rd,
- trunk/gplots/man/lowess.Rd, trunk/gplots/man/textplot.Rd,
- trunk/gplots/man/wapply.Rd, trunk/gtools/man/foldchange.Rd: -
+ * trunk/gdata/man/elem.Rd, trunk/gdata/man/ll.Rd, man/lowess.Rd,
+ man/textplot.Rd, man/wapply.Rd, trunk/gtools/man/foldchange.Rd: -
match function argument defaults with 'usage'
2003-12-03 02:42 warnes
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd: - Fix
- buglets in heatmap function
+ * R/heatmap.2.R, man/heatmap.2.Rd: - Fix buglets in heatmap
+ function
- Make a slight enhancement to the example code.
2003-12-02 22:49 warnes
- * trunk/gplots/R/heatmap.2.R: Integrated some suggestions from
- Sean Davis <sd...@ma...>.
+ * R/heatmap.2.R: Integrated some suggestions from Sean Davis
+ <sd...@ma...>.
2003-12-02 18:22 warnes
- * trunk/gplots/man/heatmap.2.Rd: - Make final example use 16
- colors instead of 8. This looks nicer.
+ * man/heatmap.2.Rd: - Make final example use 16 colors instead of
+ 8. This looks nicer.
2003-12-02 16:58 warnes
- * trunk/gplots/man/barplot2.Rd: - Remove '%' character from
- example code to avoid errors.
+ * man/barplot2.Rd: - Remove '%' character from example code to
+ avoid errors.
2003-12-02 16:54 warnes
- * trunk/gplots/R/plotCI.R: - Add '...' parameter to call to text
- to allow user to control size/color/etc.
+ * R/plotCI.R: - Add '...' parameter to call to text to allow user
+ to control size/color/etc.
2003-12-01 16:00 warnes
- * trunk/gplots/man/barplot2.Rd: - updated to match changes to
- barplot() in base.
+ * man/barplot2.Rd: - updated to match changes to barplot() in base.
2003-12-01 15:59 warnes
- * trunk/gplots/data, trunk/gplots/data/rtPCR.rda: - Renamed
- rtPCR.Rda to rtPCR.rda so that R will properly load the file
+ * data, data/rtPCR.rda: - Renamed rtPCR.Rda to rtPCR.rda so that R
+ will properly load the file
when data(rtPCR) is executed.
2003-12-01 15:55 warnes
- * trunk/gplots/R/barplot2.R: - Follow patches applied to barplot()
- in base.
+ * R/barplot2.R: - Follow patches applied to barplot() in base.
2003-11-24 21:32 warnes
- * trunk/gplots/man/heatmap.2.Rd: Fix unbalanced braces.
+ * man/heatmap.2.Rd: Fix unbalanced braces.
2003-11-24 15:09 warnes
- * trunk/gplots/R/overplot.R, trunk/gplots/man/overplot.Rd: Fix
- errors reported by R CMD check.
+ * R/overplot.R, man/overplot.Rd: Fix errors reported by R CMD
+ check.
2003-11-21 23:13 warnes
- * trunk/gplots/man/overplot.Rd: Added missing closing brace.
+ * man/overplot.Rd: Added missing closing brace.
2003-11-21 23:08 warnes
- * trunk/gplots/man/rtPCR.Rd: Initial addition of these files.
- Used in examples of overplot().
+ * man/rtPCR.Rd: Initial addition of these files. Used in examples
+ of overplot().
2003-11-21 22:59 warnes
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd:
- Applied my enhancements to the heatmap() code from R 1.8.0, and
- added
+ * R/heatmap.2.R, man/heatmap.2.Rd: Applied my enhancements to the
+ heatmap() code from R 1.8.0, and added
documentation of these changes.
2003-11-21 22:58 warnes
- * trunk/gplots/R/overplot.R, trunk/gplots/man/overplot.Rd: -
- Discovered that axis(N) does the right thing without needing to
- be
- given location for tick marks. This allowed simplification of
- the code.
+ * R/overplot.R, man/overplot.Rd: - 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
@@ -983,30 +1000,29 @@
2003-11-21 19:50 warnes
- * trunk/gplots/R/heatmap.2.R, trunk/gplots/man/heatmap.2.Rd: -
- Integrated my extensions into the R 1.8.0 version of heatmap.
+ * R/heatmap.2.R, man/heatmap.2.Rd: - Integrated my extensions into
+ the R 1.8.0 version of heatmap.
- Add Rd documentation.
2003-11-19 14:52 warnes
- * trunk/gplots/man/bandplot.Rd: Remove extranious NULL that
- confused R CMD check.
+ * man/bandplot.Rd: Remove extranious NULL that confused R CMD
+ check.
2003-11-18 18:59 warnes
- * trunk/gplots/man/barplot2.Rd: - Tiny fix to remove R CMD check
- error.
+ * man/barplot2.Rd: - Tiny fix to remove R CMD check error.
2003-11-18 18:58 warnes
- * trunk/gplots/man/smartlegend.Rd: - Added missing closing brace.
+ * man/smartlegend.Rd: - Added missing closing brace.
2003-11-18 18:45 warnes
* trunk/gdata/R/elem.R, trunk/gdata/R/env.R,
trunk/gdata/R/is.what.R, trunk/gdata/R/keep.R,
- trunk/gdata/R/ll.R, trunk/gplots/R/overplot.R: - Convert from
- MS-Dos to Unix line endings.
+ trunk/gdata/R/ll.R, R/overplot.R: - Convert from MS-Dos to Unix
+ line endings.
- Reformat to 80 columns.
2003-11-10 22:11 warnes
@@ -1015,61 +1031,56 @@
trunk/gdata/R/is.what.R, trunk/gdata/R/keep.R,
trunk/gdata/R/ll.R, trunk/gdata/man/elem.Rd,
trunk/gdata/man/env.Rd, trunk/gdata/man/is.what.Rd,
- trunk/gdata/man/keep.Rd, trunk/gdata/man/ll.Rd,
- trunk/gplots/R/heatmap.2.R, trunk/gplots/R/overplot.R,
- trunk/gplots/R/plotmeans.R, trunk/gplots/R/space.R,
- trunk/gplots/R/wapply.R, trunk/gregmisc/DESCRIPTION,
- trunk/gtools/R/capture.R, trunk/gtools/man/capture.Rd: - Add
- files contributed by Arni Magnusson
+ trunk/gdata/man/keep.Rd, trunk/gdata/man/ll.Rd, R/heatmap.2.R,
+ R/overplot.R, R/plotmeans.R, R/space.R, R/wapply.R,
+ trunk/gregmisc/DESCRIPTION, trunk/gtools/R/capture.R,
+ trunk/gtools/man/capture.Rd: - Add files contributed by Arni
+ Magnusson
<arnima@u.washington.edu>. As well as some of my own.
2003-08-19 14:58 warnes
- * trunk/gplots/R/heatmap.2.R: - Copy of local changes.
+ * R/heatmap.2.R: - Copy of local changes.
2003-08-19 14:57 warnes
- * trunk/gplots/R/heatmap.2.R: - Checkin before re-integrating
- local changes.
+ * R/heatmap.2.R: - Checkin before re-integrating local changes.
2003-06-19 21:23 warnes
- * trunk/gplots/R/heatmap.2.R: - Added enhanced heatmap function.
+ * R/heatmap.2.R: - Added enhanced heatmap function.
2003-06-09 15:10 warnes
- * trunk/gplots/man/smartlegend.Rd: - Add help text for smartlegend.
+ * man/smartlegend.Rd: - Add help text for smartlegend.
2003-06-09 14:57 warnes
- * trunk/gplots/R/smartlegend.R: - New function smartlegend().
+ * R/smartlegend.R: - New function smartlegend().
2003-04-22 17:28 warnes
- * trunk/gplots/R/plotmeans.R: - Fixeed warning messing caused when
- 'connect' is a vector.
+ * R/plotmeans.R: - Fixeed warning messing caused when 'connect' is
+ a vector.
2003-04-22 15:34 warnes
- * trunk/gplots/R/barplot2.R: Update from Marc Schwartz, modified
- by Gregory Warnes:
+ * R/barplot2.R: 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.
+ to remove R v1.7.0 if() based error msgs for vector conditions.
2003-04-04 13:49 warnes
- * trunk/gplots/R/balloonplot.R, trunk/gplots/man/qqnorm.aov.Rd,
- trunk/gtools/R/dirichlet.R: - Change occurences of 'T' to 'TRUE'
+ * R/balloonplot.R, man/qqnorm.aov.Rd, trunk/gtools/R/dirichlet.R: -
+ Change occurences of 'T' to 'TRUE'
2003-04-04 13:44 warnes
- * trunk/gplots/man/textplot.Rd: - Updated to match changes in
- textplot function:
+ * man/textplot.Rd: - Updated to match changes in textplot function:
- Added textplot.character
- - Renamed arguments "col.margin" and "row.margin" to "cmar",
- and
+ - 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
@@ -1077,65 +1088,62 @@
2003-04-04 13:41 warnes
- * trunk/gplots/R/textplot.R: - Added textplot.character to handle
- character strings.
+ * R/textplot.R: - 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 22:29 warnes
- * trunk/gplots/R/textplot.R, trunk/gplots/man/textplot.Rd: - Added
- textplot function and friends, as well as documentation.
+ * R/textplot.R, man/textplot.Rd: - Added textplot function and
+ friends, as well as documentation.
2003-03-08 16:30 warnes
- * trunk/gplots/man/balloonplot.Rd: - Forgot to update arglist in
- \usage section.
+ * man/balloonplot.Rd: - Forgot to update arglist in \usage section.
2003-03-08 16:22 warnes
- * trunk/gplots/R/balloonplot.R, trunk/gplots/man/balloonplot.Rd: -
- Added parameters for rotation of and amount of space allocated
- for
+ * R/balloonplot.R, man/balloonplot.Rd: - Added parameters for
+ rotation of and amount of space allocated for
the row and column labels.
2003-03-07 15:48 warnes
- * trunk/gmodels/R/fast.prcomp.R, trunk/gplots/R/hist2d.R,
- trunk/gplots/R/qqnorm.aov.R, trunk/gregmisc/DESCRIPTION,
- trunk/gtools/R/RSCompat.S: - Minor changes to code to allow the
- package to be provided as an
+ * trunk/gmodels/R/fast.prcomp.R, R/hist2d.R, R/qqnorm.aov.R,
+ trunk/gregmisc/DESCRIPTION, trunk/gtools/R/RSCompat.S: - Minor
+ changes to code to allow the package to be provided as an
S-Plus chapter.
2003-03-07 15:43 warnes
- * trunk/gplots/R/lowess.R: - Add 'NULL' as the last element of if
- statement that defines
+ * R/lowess.R: - 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.
2003-03-07 15:41 warnes
- * trunk/gplots/R/lowess.R: - Specify where the defualt lowess
- function should be found.
+ * R/lowess.R: - Specify where the defualt lowess function should be
+ found.
- Use getFunction in S-Plus instead of 'get'
2003-01-30 21:43 warnes
- * trunk/gplots/R/barplot2.R, trunk/gplots/man/barplot2.Rd: - Added
- argument 'add' to allow for the addition of a barplot to an
+ * R/barplot2.R, man/barplot2.Rd: - Added argument 'add' to allow
+ for the addition of a barplot to an
existing graphic. Default is FALSE
2003-01-20 18:35 warnes
- * trunk/gplots/R/balloonplot.R, trunk/gplots/man/balloonplot.Rd: -
- Updated balloonplot help page.
+ * R/balloonplot.R, man/balloonplot.Rd: - Updated balloonplot help
+ page.
2003-01-20 17:13 warnes
- * trunk/gplots/R/wapply.R, trunk/gplots/man/wapply.Rd: - Updated
- wapply.R to allow specification of evaluation points when
+ * R/wapply.R, man/wapply.Rd: - 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
@@ -1144,62 +1152,58 @@
2003-01-03 21:34 warnes
- * trunk/gplots/R/balloonplot.R, trunk/gplots/man/balloonplot.Rd: -
- Initial checkin of balloonplot functions and documentation.
+ * R/balloonplot.R, man/balloonplot.Rd: - Initial checkin of
+ balloonplot functions and documentation.
2003-01-03 19:23 warnes
- * trunk/gplots/man/space.Rd: - Added reference to and comparison
- example of sunflowerplot.
+ * man/space.Rd: - Added reference to and comparison example of
+ sunflowerplot.
- Added code to put example plots on same plot window using
par(mfrow=...).
2003-01-02 16:09 warnes
- * trunk/gplots/R/barplot2.R: - Changed assignment statements that
- used "=" to "<-" to avoid syntax
+ * R/barplot2.R: - Changed assignment statements that used "=" to
+ "<-" to avoid syntax
errors in older versions of the S language.
2003-01-02 16:07 warnes
- * trunk/gplots/R/lowess.R: - Added wrapper code so that R-specific
- fiddling won't be executed
+ * R/lowess.R: - Added wrapper code so that R-specific fiddling
+ won't be executed
under S-Plus.
2003-01-02 15:40 warnes
- * trunk/gplots/R/qqnorm.aov.R, trunk/gplots/man/qqnorm.aov.Rd: -
- Renamed first parameter to match qqnorm generic.
+ * R/qqnorm.aov.R, man/qqnorm.aov.Rd: - Renamed first parameter to
+ match qqnorm generic.
2003-01-02 15:14 warnes
- * trunk/gplots/man/qqnorm.aov.Rd: Added additional help text from
- Kjeitl.
+ * man/qqnorm.aov.Rd: Added additional help text from Kjeitl.
2002-12-31 19:50 warnes
- * trunk/gplots/R/qqnorm.aov.R, trunk/gplots/man/qqnorm.aov.Rd:
- Initial checkin of qqnorm.aov function and documentation
- submitted by
+ * R/qqnorm.aov.R, man/qqnorm.aov.Rd: Initial checkin of qqnorm.aov
+ function and documentation submitted by
Kjetil Halvorsen <kj...@ju...>.
2002-11-04 14:21 warnes
- * trunk/gplots/R/barplot2.R, trunk/gplots/man/barplot2.Rd: Updates
- from Marc Schwartz:
+ * R/barplot2.R, man/barplot2.Rd: Updates from Marc Schwartz:
- - Updated underlying code to be based upon the new barplot() in
- R v1.6.1
+ - 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
+ 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.
@@ -1207,23 +1211,22 @@
2002-10-30 02:21 warnes
- * trunk/gplots/R/plot.lm.R: - Commented out plot.lm() code since
- recent changes in R have broken it.
+ * R/plot.lm.R: - Commented out plot.lm() code since recent changes
+ in R have broken it.
2002-10-11 18:02 warnes
- * trunk/gplots/R/barplot2.R: - Fixed log scale errors in legend()
- call
+ * R/barplot2.R: - Fixed log scale errors in legend() call
2002-10-01 18:16 warnes
- * trunk/gplots/man/hist2d.Rd: - Added examples of using 'contour'
- and 'filled.contour' for display.
+ * man/hist2d.Rd: - Added examples of using 'contour' and
+ 'filled.contour' for display.
2002-09-24 14:53 warnes
- * trunk/gplots/R/plotmeans.R: - Changed digits=options("digits")
- which produces a list of length 1
+ * R/plotmeans.R: - 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().
@@ -1231,10 +1234,10 @@
2002-09-23 14:27 warnes
* trunk/gmodels/man/CrossTable.Rd, trunk/gmodels/man/glh.test.Rd,
- trunk/gplots/man/barplot2.Rd: - Fixed syntax errors in
- barplot2.Rd and CrossTable.Rd
- - Fixed incorrect translation of 'F' (distribution) to 'FALSE'
- in glh.test.Rd
+ man/barplot2.Rd: - Fixed syntax errors in barplot2.Rd and
...
[truncated message content] |
|
From: <wa...@us...> - 2007-02-08 21:56:29
|
Revision: 1050
http://svn.sourceforge.net/r-gregmisc/?rev=1050&view=rev
Author: warnes
Date: 2007-02-08 13:56:22 -0800 (Thu, 08 Feb 2007)
Log Message:
-----------
Add col2rgb() function to convert color names to rgb hex codes
Added Paths:
-----------
trunk/gplots/R/col2hex.R
trunk/gplots/man/col2hex.Rd
Added: trunk/gplots/R/col2hex.R
===================================================================
--- trunk/gplots/R/col2hex.R (rev 0)
+++ trunk/gplots/R/col2hex.R 2007-02-08 21:56:22 UTC (rev 1050)
@@ -0,0 +1,9 @@
+col2hex <- function(cname)
+ {
+ colMat <- col2rgb(cname)
+ rgb(
+ red=colMat[1,]/255,
+ blue=colMat[2,]/255,
+ green=colMat[3,]/255
+ )
+ }
Added: trunk/gplots/man/col2hex.Rd
===================================================================
--- trunk/gplots/man/col2hex.Rd (rev 0)
+++ trunk/gplots/man/col2hex.Rd 2007-02-08 21:56:22 UTC (rev 1050)
@@ -0,0 +1,24 @@
+\name{col2hex}
+\alias{col2hex}
+\title{Convert color names to hex RGB strings}
+\description{
+ Convert color names to hex RGB strings
+}
+\usage{
+col2hex(cname)
+}
+\arguments{
+ \item{cname}{Color name(s)}
+}
+\value{
+ Character vector giving the hex color code translation of the provided
+ color names.
+}
+\author{Gregory R. Warnes}
+\seealso{
+ \code{\link{col2rgb}}, \code{\link{colors}}, \code{\link{rgb}}
+ }
+\examples{
+col2hex(c("red","yellow","lightgrey"))
+}
+\keyword{color}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2007-08-14 18:48:39
|
Revision: 1140
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1140&view=rev
Author: warnes
Date: 2007-08-14 11:48:36 -0700 (Tue, 14 Aug 2007)
Log Message:
-----------
Augment balloonplot() with control of character size and color for text and label items
Modified Paths:
--------------
trunk/gplots/R/balloonplot.R
trunk/gplots/man/balloonplot.Rd
Modified: trunk/gplots/R/balloonplot.R
===================================================================
--- trunk/gplots/R/balloonplot.R 2007-08-14 18:11:33 UTC (rev 1139)
+++ trunk/gplots/R/balloonplot.R 2007-08-14 18:48:36 UTC (rev 1140)
@@ -31,9 +31,13 @@
dotsize=2/max(strwidth(19),strheight(19)),
dotchar=19,
dotcolor="skyblue",
+ text.size=1,
+ text.color=par("fg"),
main,
label=TRUE,
label.digits=2,
+ label.size=1,
+ label.color=par("fg"),
scale.method=c("volume","diameter"),
colsrt=par("srt"),
rowsrt=par("srt"),
@@ -146,7 +150,7 @@
####
## Function to scale circles to fill the containing box
####
- scale <- function(X, min=0, max=16, scale.method)
+ myscale <- function(X, min=0, max=16, scale.method)
{
if(scale.method=="volume")
{
@@ -154,7 +158,12 @@
X <- sqrt(X)
}
- X <- min + (X/max(X, na.rm=TRUE) * (max - min) )
+ # put min to 0
+ X <- (X-min(X, na.rm=TRUE))
+ # put max to 1
+ X <- X / max(X, na.rm=TRUE )
+ # now to [min,max]
+ X <- min + X * (max - min)
cin.x <- par("cin")[1]
cin.y <- par("cin")[2]
if(cin.x < cin.y) X <- X * cin.x/cin.y
@@ -205,7 +214,7 @@
plot(x=nlabels.y*rowmar+0.25 + as.numeric(ztab$x) - 1,
y=nlevels(y) - as.numeric(ztab$y) + 1,
- cex=scale(ztab$z, max=dotsize, scale.method=scale.method),
+ cex=myscale(ztab$z, max=dotsize, scale.method=scale.method),
pch=dotchar, # plot character
col=as.character(ztab$dotcolor), # dot color
xlab="",
@@ -237,7 +246,9 @@
labels=format(c(sumz, rowsumz), digits=label.digits)[-1],
font=1,
cex=par("cex")*0.75,
- adj=c(0.5,0.0)
+ adj=c(0.5,0.0),
+ col=text.color,
+ cex=text.size
)
## row totals
@@ -249,7 +260,9 @@
labels=rowlabs,
font=1,
cex=par("cex")*0.75,
- adj=c(1.0,0.5)
+ adj=c(1.0,0.5),
+ col=text.color,
+ cex=text.size
)
## overall total
@@ -259,7 +272,9 @@
labels=sumz,
font=1,
cex=par("cex")*0.75,
- adj=c(1.0,0.0)
+ adj=c(1.0,0.0),
+ col=text.color,
+ cex=text.size
)
}
@@ -331,7 +346,9 @@
y= y,
labels=undupe(xlabs[,i]),
srt=colsrt,
- font=1
+ font=1,
+ col=text.color,
+ cex=text.size
)
}
@@ -345,7 +362,9 @@
x= (i-0.5)*rowmar-0.5,
labels=undupe(ylabs[,i]),
srt=rowsrt,
- font=1
+ font=1,
+ col=text.color,
+ cex=text.size
)
}
@@ -359,7 +378,9 @@
labels=ynames,
srt=colsrt,
font=2,
- adj=c(0.5,0.0)
+ adj=c(0.5,0.0),
+ col=text.color,
+ cex=text.size
)
else
text(
@@ -368,7 +389,9 @@
labels=ylab,
srt=colsrt,
font=2,
- adj=c(0.5,0.0)
+ adj=c(0.5,0.0),
+ col=text.color,
+ cex=text.size
)
####
@@ -381,7 +404,9 @@
labels=xnames,
srt=colsrt,
font=2,
- adj=c(1,0.5)
+ adj=c(1,0.5),
+ col=text.color,
+ cex=text.size
)
else
text(
@@ -390,7 +415,9 @@
labels=xlab,
srt=colsrt,
font=2,
- adj=c(1,0.5)
+ adj=c(1,0.5),
+ col=text.color,
+ cex=text.size
)
###
@@ -426,9 +453,10 @@
text(x=as.numeric(ztab$x[indiv])+ nlabels.y*rowmar - 0.75, # as.numeric give numeric values
y=ny - as.numeric(ztab$y[indiv]) + 1,
labels=format(ztab$z[indiv], digits=label.digits), # label value
- col="black", # text color
font=2,
- adj=c(0.5,0.5)
+ adj=c(0.5,0.5),
+ col=label.color,
+ cex=label.size
)
}
# put a nice title
Modified: trunk/gplots/man/balloonplot.Rd
===================================================================
--- trunk/gplots/man/balloonplot.Rd 2007-08-14 18:11:33 UTC (rev 1139)
+++ trunk/gplots/man/balloonplot.Rd 2007-08-14 18:48:36 UTC (rev 1140)
@@ -18,9 +18,13 @@
dotsize=2/max(strwidth(19),strheight(19)),
dotchar=19,
dotcolor="skyblue",
+ text.size=1,
+ text.color=par("fg"),
main,
label=TRUE,
label.digits=2,
+ label.size=1,
+ label.color=par("fg"),
scale.method=c("volume","diameter"),
colsrt=par("srt"),
rowsrt=par("srt"),
@@ -54,10 +58,13 @@
page for the points function for symbol codes.}
\item{dotcolor}{Scalar or vector specifying the color(s) of the dots in
the plot.}
+ \item{text.size, text.color}{Character size and color for row and
+ column headers}
\item{main}{Plot title text.}
\item{label}{Boolean flag indicating whether the actual value of the
elements should be shown on the plot.}
\item{label.digits}{Number of digits used in formatting value labels.}
+ \item{label.size, label.color}{ Character size and color for value labels.}
\item{scale.method}{Method of scaling the sizes of the dot, either
"volume" or "diameter". See below.}
\item{rowsrt, colsrt}{Angle of rotation for row and column labels.}
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|
|
From: <wa...@us...> - 2007-11-01 20:18:31
|
Revision: 1212
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1212&view=rev
Author: warnes
Date: 2007-11-01 13:18:30 -0700 (Thu, 01 Nov 2007)
Log Message:
-----------
Minor reformatting of overplot code and docs
Modified Paths:
--------------
trunk/gplots/R/overplot.R
trunk/gplots/man/overplot.Rd
Modified: trunk/gplots/R/overplot.R
===================================================================
--- trunk/gplots/R/overplot.R 2007-11-01 16:42:49 UTC (rev 1211)
+++ trunk/gplots/R/overplot.R 2007-11-01 20:18:30 UTC (rev 1212)
@@ -21,7 +21,8 @@
log='',
panel='panel.overplot',
subset,
- plot=TRUE, groups,
+ plot=TRUE,
+ groups,
main,
f=2/3,
... )
Modified: trunk/gplots/man/overplot.Rd
===================================================================
--- trunk/gplots/man/overplot.Rd 2007-11-01 16:42:49 UTC (rev 1211)
+++ trunk/gplots/man/overplot.Rd 2007-11-01 20:18:30 UTC (rev 1212)
@@ -56,7 +56,8 @@
A copy of the data split by the conditioning variable.
}
\author{ Gregory R. Warnes \email{wa...@bs...} }
-\seealso{ \code{\link[base]{interaction.plot}},
+\seealso{
+ \code{\link[base]{interaction.plot}},
\code{\link[base]{coplot}} for alternative visualizations of 3-way data.}
\examples{
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|
|
From: <wa...@us...> - 2007-11-01 20:20:11
|
Revision: 1213
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1213&view=rev
Author: warnes
Date: 2007-11-01 13:20:10 -0700 (Thu, 01 Nov 2007)
Log Message:
-----------
in textplot(), convert tab characters to spaces before processing to avoid problems with computing height and width of text including tabs when using pdf()
Modified Paths:
--------------
trunk/gplots/ChangeLog
trunk/gplots/DESCRIPTION
trunk/gplots/R/textplot.R
Added Paths:
-----------
trunk/gplots/R/replaceTabs.R
Modified: trunk/gplots/ChangeLog
===================================================================
--- trunk/gplots/ChangeLog 2007-11-01 20:18:30 UTC (rev 1212)
+++ trunk/gplots/ChangeLog 2007-11-01 20:20:10 UTC (rev 1213)
@@ -1,3 +1,92 @@
+2007-11-01 20:18 warnes
+
+ * R/overplot.R, man/overplot.Rd: Minor reformatting of overplot
+ code and docs
+
+2007-10-22 02:24 warnes
+
+ * branches/GenerateFORMATSfromFactorObjects/SASxport/DESCRIPTION,
+ trunk/MSOfficeUtil/DESCRIPTION, trunk/RMCMC/DESCRIPTION,
+ trunk/Rlsf/DESCRIPTION, trunk/SASxport/DESCRIPTION,
+ trunk/bwRF/DESCRIPTION, trunk/exp.ssize/DESCRIPTION,
+ trunk/fork/DESCRIPTION, trunk/gdata/DESCRIPTION,
+ trunk/gmodels/DESCRIPTION, DESCRIPTION,
+ trunk/gregmisc/DESCRIPTION, trunk/ssize/DESCRIPTION: Clarify GPL
+ version
+
+2007-08-14 19:14 warnes
+
+ * R/balloonplot.R: Correct error in balloonplot when z contains NA
+ values.
+
+2007-08-14 18:48 warnes
+
+ * R/balloonplot.R, man/balloonplot.Rd: Augment balloonplot() with
+ control of character size and color for text and label items
+
+2007-08-14 18:11 warnes
+
+ * R/balloonplot.R: Correct balloonplot.default to properly show
+ specified x and y axis labels when explicitly provided
+
+2007-03-09 09:05 ggorjan
+
+ * man/ooplot.Rd: 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 23:05 warnes
+
+ * DESCRIPTION: Bump version number
+
+2007-02-08 22:03 warnes
+
+ * man/textplot.Rd: Update documentation for textplot()
+
+2007-02-08 21:56 warnes
+
+ * R/col2hex.R, man/col2hex.Rd: Add col2rgb() function to convert
+ color names to rgb hex codes
+
+2007-02-08 21:32 warnes
+
+ * R/textplot.R: 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.
+
+2007-02-08 16:56 warnes
+
+ * R/bandplot.R: Add parameters to control line width and line type.
+
+2006-11-14 22:25 ggorjan
+
+ * trunk/gdata/man/combine.Rd, trunk/gdata/man/frameApply.Rd,
+ trunk/gmodels/R/ci.R, trunk/gmodels/R/fast.prcomp.R,
+ trunk/gmodels/man/ci.Rd, R/bandplot.R, R/boxplot.n.R, R/lowess.R,
+ R/plot.lm.R, R/plotCI.R, R/plotmeans.R, R/residplot.R,
+ R/wapply.R, man/boxplot.n.Rd, man/plotCI.Rd, man/plotmeans.Rd,
+ trunk/gtools/R/combinations.R, trunk/gtools/R/running.R,
+ trunk/gtools/man/ELISA.Rd, trunk/gtools/man/combinations.Rd:
+ Removed executable property
+
+2006-11-14 18:29 warnes
+
+ * tests/heatmap2Test.Rout.save: Update output file to match
+ (trivial) changes in the test code.
+
+2006-11-14 18:07 warnes
+
+ * ChangeLog, NEWS: Update ChangeLog and NEWS files for release
+ 2.3.2.
+
+2006-11-14 17:59 warnes
+
+ * DESCRIPTION: Update version number
+
+2006-11-14 17:57 warnes
+
+ * DESCRIPTION: Update version number and maintainer
+
2006-11-14 17:56 warnes
* man/heatmap.2.Rd: Correct problem with labeled correlation matrix
Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION 2007-11-01 20:18:30 UTC (rev 1212)
+++ trunk/gplots/DESCRIPTION 2007-11-01 20:20:10 UTC (rev 1213)
@@ -4,7 +4,7 @@
Depends: R (>= 1.9.0), gtools, gdata, stats
Recommends: datasets
Suggests: gtools, gdata
-Version: 2.4.0
+Version: 2.4.1
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker and Thomas Lumley
Maintainer: Gregory R. Warnes <wa...@bs...>
Added: trunk/gplots/R/replaceTabs.R
===================================================================
--- trunk/gplots/R/replaceTabs.R (rev 0)
+++ trunk/gplots/R/replaceTabs.R 2007-11-01 20:20:10 UTC (rev 1213)
@@ -0,0 +1,35 @@
+## Function to replace all tabs in a string with an appropriate number of spaces.
+
+# handle a single character string
+replaceTabs.inner <- function( text, width=8 )
+{
+ spaces <- " "
+
+ if(nchar(text)<1) return(text)
+
+ text.split <- strsplit(text,"\t")[[1]]
+ if(length(text.split)==1)
+ return(text)
+ else
+ {
+ nSpaceAdd <- 8 - nchar(text.split) %% 8
+ nSpaceAdd[length(nSpaceAdd)] <- 0
+ nSpaceAdd[nSpaceAdd==8] <- 0
+
+ retval <- ""
+ for(i in 1:length(text.split))
+ {
+ tmp.text <- chartr("\t"," ", text.split[i]) # one space here
+ retval <- paste(retval, tmp.text, substr(spaces,0,nSpaceAdd[i]-1 ), sep='' ) # rest here
+ }
+ return(retval)
+ }
+}
+
+replaceTabs <- function(text, width=8)
+{
+ text <- as.character(text)
+ retval <- sapply(text, replaceTabs.inner)
+ names(retval) <- names(text)
+ retval
+}
Modified: trunk/gplots/R/textplot.R
===================================================================
--- trunk/gplots/R/textplot.R 2007-11-01 20:18:30 UTC (rev 1212)
+++ trunk/gplots/R/textplot.R 2007-11-01 20:20:10 UTC (rev 1213)
@@ -182,9 +182,11 @@
cspace=1,
lspace=1,
mar=c(0,0,3,0)+0.1,
+ tab.width=8,
...)
{
object <- paste(object,collapse="\n",sep="")
+ object <- replaceTabs(object, width=tab.width)
halign = match.arg(halign)
valign = match.arg(valign)
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|
|
From: <wa...@us...> - 2007-11-02 18:22:37
|
Revision: 1217
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1217&view=rev
Author: warnes
Date: 2007-11-02 11:22:36 -0700 (Fri, 02 Nov 2007)
Log Message:
-----------
Create soft links of gmodels/ChangeLog -> gmodels/inst/ChangeLog, and gmodels/NEWS -> gmodels/inst/NEWS for my convenience
Added Paths:
-----------
trunk/gplots/ChangeLog
trunk/gplots/NEWS
Added: trunk/gplots/ChangeLog
===================================================================
--- trunk/gplots/ChangeLog (rev 0)
+++ trunk/gplots/ChangeLog 2007-11-02 18:22:36 UTC (rev 1217)
@@ -0,0 +1 @@
+link inst/ChangeLog
\ No newline at end of file
Property changes on: trunk/gplots/ChangeLog
___________________________________________________________________
Name: svn:special
+ *
Added: trunk/gplots/NEWS
===================================================================
--- trunk/gplots/NEWS (rev 0)
+++ trunk/gplots/NEWS 2007-11-02 18:22:36 UTC (rev 1217)
@@ -0,0 +1 @@
+link inst/NEWS
\ No newline at end of file
Property changes on: trunk/gplots/NEWS
___________________________________________________________________
Name: svn:special
+ *
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <wa...@us...> - 2008-04-07 16:47:38
|
Revision: 1252
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1252&view=rev
Author: warnes
Date: 2008-04-07 09:47:30 -0700 (Mon, 07 Apr 2008)
Log Message:
-----------
Add ability to control location of individual heatmap.2 components
Modified Paths:
--------------
trunk/gplots/R/heatmap.2.R
trunk/gplots/man/heatmap.2.Rd
Modified: trunk/gplots/R/heatmap.2.R
===================================================================
--- trunk/gplots/R/heatmap.2.R 2008-03-27 22:36:13 UTC (rev 1251)
+++ trunk/gplots/R/heatmap.2.R 2008-04-07 16:47:30 UTC (rev 1252)
@@ -62,6 +62,11 @@
xlab = NULL,
ylab = NULL,
+ # plot layout
+ lmat = NULL,
+ lhei = NULL,
+ lwid = NULL,
+
# extras
...
)
@@ -270,23 +275,45 @@
x[] <- ifelse(x<min.breaks, min.breaks, x)
x[] <- ifelse(x>max.breaks, max.breaks, x)
+
+
+
+
+
## Calculate the plot layout
- lmat <- rbind(4:3, 2:1)
- lhei <- lwid <- c(keysize, 4)
- if(!missing(ColSideColors)) { ## add middle row to layout
- if(!is.character(ColSideColors) || length(ColSideColors) != nc)
- stop("'ColSideColors' must be a character vector of length ncol(x)")
- lmat <- rbind(lmat[1,]+1, c(NA,1), lmat[2,]+1)
- lhei <- c(lhei[1], 0.2, lhei[2])
- }
- if(!missing(RowSideColors)) { ## add middle column to layout
- if(!is.character(RowSideColors) || length(RowSideColors) != nr)
- stop("'RowSideColors' must be a character vector of length nrow(x)")
- lmat <- cbind(lmat[,1]+1, c(rep(NA, nrow(lmat)-1), 1), lmat[,2]+1)
- lwid <- c(lwid[1], 0.2, lwid[2])
- }
- lmat[is.na(lmat)] <- 0
+ if( missing(lhei) || is.null(lhei) )
+ lhei <- c(keysize, 4)
+ if( missing(lwid) || is.null(lwid) )
+ lwid <- c(keysize, 4)
+
+ if( missing(lmat) || is.null(lmat) )
+ {
+ lmat <- rbind(4:3, 2:1)
+
+ if(!missing(ColSideColors)) { ## add middle row to layout
+ if(!is.character(ColSideColors) || length(ColSideColors) != nc)
+ stop("'ColSideColors' must be a character vector of length ncol(x)")
+ lmat <- rbind(lmat[1,]+1, c(NA,1), lmat[2,]+1)
+ lhei <- c(lhei[1], 0.2, lhei[2])
+ }
+
+ if(!missing(RowSideColors)) { ## add middle column to layout
+ if(!is.character(RowSideColors) || length(RowSideColors) != nr)
+ stop("'RowSideColors' must be a character vector of length nrow(x)")
+ lmat <- cbind(lmat[,1]+1, c(rep(NA, nrow(lmat)-1), 1), lmat[,2]+1)
+ lwid <- c(lwid[1], 0.2, lwid[2])
+ }
+
+ lmat[is.na(lmat)] <- 0
+ }
+
+ if(length(lhei) != nrow(lmat))
+ stop("lhei must have length = nrow(lmat) = ", nrow(lmat))
+
+ if(length(lwid) != ncol(lmat))
+ stop("lwid must have length = ncol(lmat) =", ncol(lmat))
+
## Graphics `output' -----------------------
op <- par(no.readonly = TRUE)
Modified: trunk/gplots/man/heatmap.2.Rd
===================================================================
--- trunk/gplots/man/heatmap.2.Rd 2008-03-27 22:36:13 UTC (rev 1251)
+++ trunk/gplots/man/heatmap.2.Rd 2008-04-07 16:47:30 UTC (rev 1252)
@@ -71,6 +71,11 @@
xlab = NULL,
ylab = NULL,
+ # plot layout
+ lmat = NULL,
+ lhei = NULL,
+ lwid = NULL,
+
# extras
...
)
@@ -180,6 +185,9 @@
0.25.}
% plot labels
\item{main, xlab, ylab}{main, x- and y-axis titles; defaults to none.}
+ % figure layout
+ \item{lmat, lhei, lwid}{visual layout: position matrix, column height,
+ column width. See below for details}
\item{...}{additional arguments passed on to \code{\link{image}} } %
}
\details{
@@ -209,7 +217,18 @@
as the \pkg{RColorBrewer} package,
\url{http://cran.r-project.org/src/contrib/PACKAGES.html#RColorBrewer}
to select better colors.
-
+
+ By default four components will be displayed in the plot. At the top
+ left is the color key, top right is the column dendogram, bottom left
+ is the row dendogram, bottom right is the image plot. When
+ RowSideColor or ColSideColor are provided, an additional row or column
+ is inserted in the appropriate location. This layout can be
+ overriden by specifiying appropriate values for \code{lmat},
+ \code{lwid}, and \code{lhei}. \code{lmat} controls the relative
+ postition of each element, while \code{lwid} controls the column
+ width, and \code{lhei} controls the row height. See the help page for
+ \code{\link[graphics]{layout}} for details on how to use these
+ arguments.
}
\note{
The original rows and columns are reordered \emph{in any case} to
@@ -276,7 +295,12 @@
# without reorder
heatmap.2(Ca, Rowv=FALSE, symm=TRUE, margin=c(6, 6), trace="none" )
+ ## Place the color key below the image plot
+ heatmap.2(x, lmat=rbind( c(0, 3), c(2,1), c(0,4) ), lhei=c(1.5, 4, 2 ) )
+ ## Place the color key to the top right of the image plot
+ heatmap.2(x, lmat=rbind( c(0, 3, 4), c(2,1,0 ) ), lwid=c(1.5, 4, 2 ) )
+
## For variable clustering, rather use distance based on cor():
data(USJudgeRatings)
symnum( cU <- cor(USJudgeRatings) )
@@ -312,5 +336,6 @@
main="SpikeIn@pm Fold Changes\nrelative to 12.50 sample",
xlab="Relative Concentration", ylab="Probeset")
}
+
}
\keyword{hplot}
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|
|
From: <wa...@us...> - 2008-04-07 16:52:53
|
Revision: 1253
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1253&view=rev
Author: warnes
Date: 2008-04-07 09:52:50 -0700 (Mon, 07 Apr 2008)
Log Message:
-----------
Updates for gplots 2.6.0
Modified Paths:
--------------
trunk/gplots/DESCRIPTION
trunk/gplots/inst/ChangeLog
trunk/gplots/inst/NEWS
Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION 2008-04-07 16:47:30 UTC (rev 1252)
+++ trunk/gplots/DESCRIPTION 2008-04-07 16:52:50 UTC (rev 1253)
@@ -4,7 +4,7 @@
Depends: R (>= 1.9.0), gtools, gdata, stats
Recommends: datasets
Suggests: gtools, gdata
-Version: 2.5.0
+Version: 2.6.0
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker and Thomas Lumley
Maintainer: Gregory R. Warnes <wa...@bs...>
Modified: trunk/gplots/inst/ChangeLog
===================================================================
--- trunk/gplots/inst/ChangeLog 2008-04-07 16:47:30 UTC (rev 1252)
+++ trunk/gplots/inst/ChangeLog 2008-04-07 16:52:50 UTC (rev 1253)
@@ -1,3 +1,51 @@
+2008-04-07 16:47 warnes
+
+ * [r1252] R/heatmap.2.R, man/heatmap.2.Rd: Add ability to control
+ location of individual heatmap.2 components
+
+2008-03-27 22:36 warnes
+
+ * [r1251] R/heatmap.2.R: Fix bug in handling rowsep, per suggestion
+ by Steven Paugh
+
+2008-01-04 18:59 warnes
+
+ * [r1238] man/overplot.Rd: Fix examples for overplot()
+
+2008-01-02 16:58 warnes
+
+ * [r1237] man/barplot2.Rd: Update Marc's email address
+
+2007-12-20 22:48 warnes
+
+ * [r1235] man/heatmap.2.Rd: Two letter clarification of help text
+ for heatmap.2()
+
+2007-12-20 22:24 warnes
+
+ * [r1234] man/ooplot.Rd: Restore plot layout at end of ooplot()
+ example
+
+2007-11-06 16:24 warnes
+
+ * [r1222] man/hist2d.Rd: Remove extraneous closing brace in the
+ hist2d documentation file
+
+2007-11-05 15:32 warnes
+
+ * [r1221] inst/NEWS: Fix typo in NEWS: col2hex() is the new
+ function, not col2rgb() which is part of grDevices
+
+2007-11-02 19:32 warnes
+
+ * [r1219] DESCRIPTION, NAMESPACE, inst/ChangeLog, inst/NEWS:
+ Updates for gplots 2.5.0
+
+2007-11-02 19:32 warnes
+
+ * [r1218] tests/heatmap2Test.Rout.save: Update saved test output
+ due to changes in how R reports warnings
+
2007-11-02 18:22 warnes
* [r1217] ChangeLog, NEWS: Create soft links of gmodels/ChangeLog
Modified: trunk/gplots/inst/NEWS
===================================================================
--- trunk/gplots/inst/NEWS 2008-04-07 16:47:30 UTC (rev 1252)
+++ trunk/gplots/inst/NEWS 2008-04-07 16:52:50 UTC (rev 1253)
@@ -1,3 +1,23 @@
+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
--------------------------
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|
|
From: <wa...@us...> - 2008-05-05 20:27:17
|
Revision: 1260
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1260&view=rev
Author: warnes
Date: 2008-05-05 13:27:11 -0700 (Mon, 05 May 2008)
Log Message:
-----------
balloonplot: Add option to scale balloons so [min,max]->[0,1] (relative) or so [0,max] <- [0,1] (absolute)
Modified Paths:
--------------
trunk/gplots/R/balloonplot.R
trunk/gplots/man/balloonplot.Rd
Modified: trunk/gplots/R/balloonplot.R
===================================================================
--- trunk/gplots/R/balloonplot.R 2008-04-12 19:42:16 UTC (rev 1259)
+++ trunk/gplots/R/balloonplot.R 2008-05-05 20:27:11 UTC (rev 1260)
@@ -39,6 +39,7 @@
label.size=1,
label.color=par("fg"),
scale.method=c("volume","diameter"),
+ scale.range=c("absolute","relative"),
colsrt=par("srt"),
rowsrt=par("srt"),
colmar=1,
@@ -74,6 +75,7 @@
####
scale.method <- match.arg(scale.method)
+ scale.range <- match.arg(scale.range)
if( any(z < 0, na.rm=TRUE ) )
warning("z value(s) below zero detected.",
@@ -150,7 +152,7 @@
####
## Function to scale circles to fill the containing box
####
- myscale <- function(X, min=0, max=16, scale.method)
+ myscale <- function(X, min=0, max=16, scale.method, scale.range)
{
if(scale.method=="volume")
{
@@ -158,12 +160,11 @@
X <- sqrt(X)
}
- # put min to 0
- X <- (X-min(X, na.rm=TRUE))
- # put max to 1
- X <- X / max(X, na.rm=TRUE )
- # now to [min,max]
- X <- min + X * (max - min)
+ if(scale.range=="relative")
+ X <- (X-min(X, na.rm=TRUE)) # put min to 0
+ X <- X / max(X, na.rm=TRUE ) # put max to 1
+ X <- min + X * (max - min) # now to [min,max]
+
cin.x <- par("cin")[1]
cin.y <- par("cin")[2]
if(cin.x < cin.y) X <- X * cin.x/cin.y
@@ -200,21 +201,21 @@
{
xlim=c(-0.5,nlevels(x)+nlabels.y*rowmar-0.25) # extra space on either
# end of plot for labels
- ylim=c(0.50,nlevels(y)+nlabels.x*colmar+1) # and so dots don't cross
+ ylim=c(0.50,nlevels(y)+nlabels.x*colmar+1) # and so dots don't cross
# into margins,
}
else
{
- xlim=c(-0.5,nlevels(x)+nlabels.y*rowmar+1) # extra space on either
+ xlim=c(-0.5,nlevels(x)+nlabels.y*rowmar+1) # extra space on either
# end of plot for labels
- ylim=c(0,nlevels(y)+nlabels.x*colmar+1) # and so dots don't cross
+ ylim=c(0,nlevels(y)+nlabels.x*colmar+1) # and so dots don't cross
# into margins,
}
plot(x=nlabels.y*rowmar+0.25 + as.numeric(ztab$x) - 1,
y=nlevels(y) - as.numeric(ztab$y) + 1,
- cex=myscale(ztab$z, max=dotsize, scale.method=scale.method),
+ cex=myscale(ztab$z, max=dotsize, scale.method=scale.method, scale.range=scale.range),
pch=dotchar, # plot character
col=as.character(ztab$dotcolor), # dot color
xlab="",
@@ -245,7 +246,6 @@
y=0.25,
labels=format(c(sumz, rowsumz), digits=label.digits)[-1],
font=1,
- cex=par("cex")*0.75,
adj=c(0.5,0.0),
col=text.color,
cex=text.size
@@ -259,7 +259,6 @@
y= (ny:1),
labels=rowlabs,
font=1,
- cex=par("cex")*0.75,
adj=c(1.0,0.5),
col=text.color,
cex=text.size
@@ -271,7 +270,6 @@
y=0.25,
labels=sumz,
font=1,
- cex=par("cex")*0.75,
adj=c(1.0,0.0),
col=text.color,
cex=text.size
@@ -371,7 +369,7 @@
####
## Column headers for row labels
####
- if(missing(ylab))
+ if(missing(ylab) || length(ylab)==0)
text(
x=((1:length(ylabs))-0.5)*rowmar-0.5,
y=ny+0.5,
@@ -397,7 +395,7 @@
####
## Row headers for column labels
####
- if(missing(xlab))
+ if(missing(xlab) || length(xlab)==0)
text(
x= nlabels.y*rowmar - 0.25 - strwidth(','),
y= ny + 0.75 + ((nlabels.x:1) - 1 + .5)*colmar,
Modified: trunk/gplots/man/balloonplot.Rd
===================================================================
--- trunk/gplots/man/balloonplot.Rd 2008-04-12 19:42:16 UTC (rev 1259)
+++ trunk/gplots/man/balloonplot.Rd 2008-05-05 20:27:11 UTC (rev 1260)
@@ -26,6 +26,7 @@
label.size=1,
label.color=par("fg"),
scale.method=c("volume","diameter"),
+ scale.range=c("absolute","relative"),
colsrt=par("srt"),
rowsrt=par("srt"),
colmar=1,
@@ -67,6 +68,11 @@
\item{label.size, label.color}{ Character size and color for value labels.}
\item{scale.method}{Method of scaling the sizes of the dot, either
"volume" or "diameter". See below.}
+ \item{scale.range}{Method for scaling original data to compute
+ circle diameter. \code{scale.range="absolute"} scales the data
+ relative to 0 (i.e, maps [0,max(z)] --> [0,1]), while
+ \code{scale.range="relative"} scales the data relative to min(z)
+ (i.e. maps [min(z), max(z)] --> [0,1]).}
\item{rowsrt, colsrt}{Angle of rotation for row and column labels.}
\item{rowmar, colmar}{Space allocated for row and column labels. Each
unit is the width/height of one cell in the table.}
@@ -166,7 +172,7 @@
balloonplot(x=list(Age,Sex),
y=list(Class=Class,
- Survived=reorder.factor(Survived,c(2,1))),
+ Survived=gdata::reorder.factor(Survived,c(2,1))),
z=Freq,
zlab="Number of Passengers",
sort=TRUE,
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|
|
From: <wa...@us...> - 2008-05-05 20:29:08
|
Revision: 1262
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1262&view=rev
Author: warnes
Date: 2008-05-05 13:28:53 -0700 (Mon, 05 May 2008)
Log Message:
-----------
Use caTools's runsd in bandplot for a dramatic speedup for large data
Modified Paths:
--------------
trunk/gplots/DESCRIPTION
trunk/gplots/R/bandplot.R
Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION 2008-05-05 20:28:00 UTC (rev 1261)
+++ trunk/gplots/DESCRIPTION 2008-05-05 20:28:53 UTC (rev 1262)
@@ -3,7 +3,7 @@
Description: Various R programming tools for plotting data
Depends: R (>= 1.9.0), gtools, gdata, stats
Recommends: datasets
-Suggests: gtools, gdata
+Suggests: gtools, gdata, caTools
Version: 2.6.0
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker and Thomas Lumley
Modified: trunk/gplots/R/bandplot.R
===================================================================
--- trunk/gplots/R/bandplot.R 2008-05-05 20:28:00 UTC (rev 1261)
+++ trunk/gplots/R/bandplot.R 2008-05-05 20:28:53 UTC (rev 1262)
@@ -6,9 +6,10 @@
sd=c(-2:2),
sd.col=c("lightblue","blue","red",
"blue","lightblue"),
- sd.lwd=c(1,2,3,2,1),
+ sd.lwd=c(2,2,3,2,2),
sd.lty=c(2,1,1,1,2),
method="frac", width=1/5,
+ use.runsd=TRUE,
n=50
)
{
@@ -16,7 +17,6 @@
if(length(sd.col)<length(sd)) sd <-rep(sd.col,length=length(sd))
if(length(sd.lwd)<length(sd)) sd <-rep(sd.lwd,length=length(sd))
if(length(sd.lty)<length(sd)) sd <-rep(sd.lty,length=length(sd))
-
if(!add)
{
m <- match.call(expand.dots = TRUE)
@@ -37,7 +37,18 @@
sdplot <- function(S, COL, LWD, LTY)
{
- where <- wapply(x,y,CL,sd=S,width=width,method=method,n=n)
+ if(use.runsd)
+ {
+ ord <- order(x)
+ myx <- x[ord]
+ myy <- y[ord]
+ sd <- runsd(myy, k=floor(length(x)*width))
+ where <- list()
+ where$x <- myx
+ where$y <- runmean(myy, k=floor(length(x)*width) ) + S * sd
+ }
+ else
+ where <- wapply(x,y,CL,sd=S,width=width,method=method,n=n)
lines(where,col=COL,lwd=LWD,lty=LTY,...)
where
}
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|
|
From: <wa...@us...> - 2008-05-07 18:59:34
|
Revision: 1264
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1264&view=rev
Author: warnes
Date: 2008-05-07 11:59:21 -0700 (Wed, 07 May 2008)
Log Message:
-----------
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.
Modified Paths:
--------------
trunk/gplots/DESCRIPTION
trunk/gplots/R/bandplot.R
Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION 2008-05-07 18:57:29 UTC (rev 1263)
+++ trunk/gplots/DESCRIPTION 2008-05-07 18:59:21 UTC (rev 1264)
@@ -1,9 +1,9 @@
Package: gplots
Title: Various R programming tools for plotting data
Description: Various R programming tools for plotting data
-Depends: R (>= 1.9.0), gtools, gdata, stats
+Depends: R (>= 1.9.0), gtools, gdata, stats, caTools
Recommends: datasets
-Suggests: gtools, gdata, caTools
+Suggests: gtools, gdata
Version: 2.6.0
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker and Thomas Lumley
Modified: trunk/gplots/R/bandplot.R
===================================================================
--- trunk/gplots/R/bandplot.R 2008-05-07 18:57:29 UTC (rev 1263)
+++ trunk/gplots/R/bandplot.R 2008-05-07 18:59:21 UTC (rev 1264)
@@ -4,8 +4,8 @@
...,
add=FALSE,
sd=c(-2:2),
- sd.col=c("lightblue","blue","red",
- "blue","lightblue"),
+ sd.col=c("magenta","blue","red",
+ "blue","magenta"),
sd.lwd=c(2,2,3,2,2),
sd.lty=c(2,1,1,1,2),
method="frac", width=1/5,
@@ -35,32 +35,22 @@
else
mean(x)+sd*sqrt(var(x))
- sdplot <- function(S, COL, LWD, LTY)
- {
- if(use.runsd)
- {
- ord <- order(x)
- myx <- x[ord]
- myy <- y[ord]
- sd <- runsd(myy, k=floor(length(x)*width))
- where <- list()
- where$x <- myx
- where$y <- runmean(myy, k=floor(length(x)*width) ) + S * sd
- }
- else
- where <- wapply(x,y,CL,sd=S,width=width,method=method,n=n)
- lines(where,col=COL,lwd=LWD,lty=LTY,...)
- where
- }
+ ord <- order(x)
+ myx <- x[ord]
+ myy <- y[ord]
+ sdVec <- runsd(myy, k=floor(length(x)*width))
+ meanVec <- runmean(myy, k=floor(length(x)*width) )
stdevs <- list()
for( i in 1:length(sd) )
- stdevs[[as.character(sd[i])]] <- sdplot(
- sd[i],
- COL=sd.col[i],
- LWD=sd.lwd[i],
- LTY=sd.lty[i]
- )
+ {
+ lines(myx,
+ meanVec + sdVec * sd[i],
+ col=sd.col[i],
+ lwd=sd.lwd[i],
+ lty=sd.lty[i]
+ )
- invisible( stdevs )
+ }
+
}
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|
|
From: <wa...@us...> - 2008-05-20 00:14:56
|
Revision: 1271
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1271&view=rev
Author: warnes
Date: 2008-05-19 17:14:51 -0700 (Mon, 19 May 2008)
Log Message:
-----------
Add Venn Diagram plot submitted by Steffen Moeller
Modified Paths:
--------------
trunk/gplots/DESCRIPTION
trunk/gplots/NAMESPACE
Added Paths:
-----------
trunk/gplots/R/venn.R
trunk/gplots/man/venn.Rd
Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION 2008-05-13 03:16:08 UTC (rev 1270)
+++ trunk/gplots/DESCRIPTION 2008-05-20 00:14:51 UTC (rev 1271)
@@ -2,10 +2,13 @@
Title: Various R programming tools for plotting data
Description: Various R programming tools for plotting data
Depends: R (>= 1.9.0), gtools, gdata, stats, caTools
-Recommends: datasets
-Suggests: gtools, gdata
-Version: 2.6.0
+Recommends: datasets, grid
+Suggests: gtools, grid
+Version: 2.7.0
Author: Gregory R. Warnes. Includes R source code and/or documentation
- contributed by Ben Bolker and Thomas Lumley
+ contributed by (in alphabetical order):
+ Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang
+ Huber Andy Liaw, Thomas Lumley, Martin Maechler, Arni
+ Magnusson, Steffen Moeller, Marc Schwartz, Bill Venables
Maintainer: Gregory R. Warnes <wa...@bs...>
License: GPL-2
Modified: trunk/gplots/NAMESPACE
===================================================================
--- trunk/gplots/NAMESPACE 2008-05-13 03:16:08 UTC (rev 1270)
+++ trunk/gplots/NAMESPACE 2008-05-20 00:14:51 UTC (rev 1271)
@@ -25,6 +25,7 @@
smartlegend,
space,
textplot,
+ venn,
wapply
)
Added: trunk/gplots/R/venn.R
===================================================================
--- trunk/gplots/R/venn.R (rev 0)
+++ trunk/gplots/R/venn.R 2008-05-20 00:14:51 UTC (rev 1271)
@@ -0,0 +1,437 @@
+# This code plots Venn Diagrams for up to 5 sets. The
+# function getVennCounts is passed a list of vectors.
+# This is transformed into a table indicating the
+# number of members for each intersection. This table
+# is generated for any number of sets.
+
+# The function drawVennDiagram plots circles (up to three
+# sets) or ellipses (4 and 5 sets) to depict the sets.
+# The sum of values placed is the number of entries of
+# each set.
+
+# transform base
+# v = value of base 10 to be transformed
+# b = new base
+# l = minimal length of returned array (default is 1)
+# return value: array of factors, highest exponent first
+baseOf<-function(v,b,l=1) {
+ remainder<-v
+ i<-l
+ ret<-NULL
+ while(remainder>0 || i>0) {
+ #print(paste("i=",i," remainder=",remainder))
+ m<-remainder%%b
+ if (is.null(ret)) {
+ ret<-m
+ }
+ else {
+ ret<-c(m,ret)
+ }
+ remainder <- remainder %/% b
+ i<-i-1
+ }
+ return(ret)
+}
+
+# Function to determine values of a venn diagram
+# It works for an arbitrary large set of input sets.
+#
+
+getVennCounts <- function(l, universe, ...)
+ UseMethod("getVennCounts")
+
+getVennCounts.data.frame <- function(l, universe=NA, ...)
+ {
+ if( !all(unique(unlist(l)) %in% c(0,1)) )
+ stop("Only indicator columns permitted")
+
+ l <- sapply( l, function(x) which(as.logical(x)))
+ getVennCounts.list(l)
+ }
+
+getVennCounts.list<-function(l,universe=NA) {
+ numSets<-length(l)
+ result.table<-NULL
+ result.table.names<-NULL
+ for (i in 0:(-1 + 2^numSets)) {
+ # i2 is a binary representation of that number
+ i2<-baseOf(i,2,numSets)
+
+ # some debug output
+ #print(paste(i,":",paste(i2,collapse="",sep="")))
+
+ # p.pos determines the position in number
+ # which is also the set that is inspected
+
+ sel<-universe
+
+ # positive selection first
+ for (p.pos in which(1 == i2) ) {
+ current.set<-l[[p.pos]]
+ #print(paste("set ",p.pos,", val=1: ",paste(current.set,collapse=",")))
+ if (is.null(sel)) {
+ #print("Sel is null")
+ } else if (1 == length(sel) && is.na(sel)) {
+ sel<-current.set
+ }
+ else {
+ w<-which(sel %in% current.set)
+ if (length(w)>0) {
+ sel<-sel[w]
+ }
+ else {
+ sel<-NULL
+ }
+ }
+ }
+
+ # something should be in sel now, otherwise
+ # the number will be 0
+
+ # negative selection
+ for (p.pos in which(0 == i2) ) {
+ if (is.null(sel) || ( 1 == length(sel) && is.na(sel))) {
+ # The complement is not known, hence no checks done
+ }
+ else {
+ current.set<-l[[p.pos]]
+ w<-which( ! sel %in% current.set)
+ #print(paste("set ",p.pos,", val=1: ",paste(current.set,collapse=",")))
+ if (length(w)>0) {
+ sel<-sel[w]
+ }
+ else {
+ sel<-NULL
+ }
+ }
+ }
+ #print(paste("sel:",paste(sel,collapse=",")))
+
+ if(is.null(sel) || (1 == length(sel) && is.na(sel))) {
+ sel<-NULL
+ }
+
+ r<-length(sel)
+ r.name<-paste(i2,collapse="")
+ result.row<-c(r,i2)
+ dim(result.row)<-c(1,length(result.row))
+ rownames(result.row)<-c(r.name)
+ #print(paste("Adding ",r.name))
+ if (is.null(result.table)) {
+ result.table<-result.row
+ }
+ else {
+ result.table<-rbind(result.table,result.row)
+ }
+ #if (is.null(result.table)) {
+ # result.table<-r
+ # result.table.names<-r.name
+ #}
+ #else {
+ # result.table<-c(result.table,r)
+ # result.table.names<-c(result.table.names,r.name)
+ #}
+ }
+ #names(result.table)<-result.table.names
+ if (is.null(names(l))) {
+ colnames(result.table)<-c("num",LETTERS[1:numSets])
+ }
+ else{
+ colnames(result.table)<-c("num",names(l))
+ }
+ return(result.table)
+}
+
+#print(getVennCounts(list(A,B,C,D)))
+#print(getVennCounts(list(a=A,b=B,c=C,d=D)))
+
+
+## data should be a matrix.
+## - The first column of the matrix is the
+## count of the number of objects with the specified pattern.
+## - The second and subsequent columns contain 0-1 indicators
+## giving the pattern of group membership
+
+
+drawVennDiagram <-function(data,small=0.7,
+ showSetLogicLabel=FALSE,simplify=FALSE) {
+ numCircles<-NA
+ data.colnames<-NULL
+ data.rownames<-NULL
+ if(is.matrix(data)) {
+ numCircles<-ncol(data)-1
+ data.colnames<-colnames(data)[2:(ncol(data))]
+ # Order is reverted since later indexing starts with
+ # the "lowest bit" and that is expected at the left
+ data.rownames<-rownames(data)
+ }
+ else {
+ cat("Testing only, presuming first argument to specify",
+ "the number of circles to draw.\n")
+ numCircles<-data
+ }
+
+ m<-(0:(-1+2^numCircles))
+
+ if (! is.matrix(data)) {
+ ##cat("prepare randomised data\n")
+ data<-t(sapply(X=m,FUN=function(v){
+ l<-baseOf(v,2,numCircles)
+ #print(l)
+ return(l)
+ }))
+
+ #print(data)
+
+ #data.names<-apply(data,1,function(X){
+ # return(paste(X),collapse="")
+ #})
+ for(i in m) {
+ n<-paste(data[i+1,],collapse="")
+ if (is.null(data.rownames)) {
+ data.rownames<-n
+ }
+ else {
+ data.rownames<-c(data.rownames,n)
+ }
+ }
+ #print(data.rownames)
+ data<-cbind(sample(1:100,size=2^numCircles,replace=TRUE),data)
+ #print(data)
+ rownames(data)<-data.rownames
+ data.colnames<-LETTERS[1:numCircles]
+ colnames(data)<-c("num",data.colnames)
+ }
+
+ if ((2 <= numCircles && numCircles <= 3) || (4 == numCircles && simplify)) {
+ ##cat("drawing circles\n")
+ # draw circles with radius 1.7 equally distributed
+ # with centers on a circle of radius 1
+
+ degrees<-2*pi/numCircles*(1:numCircles)
+
+ # scaling factor
+ s<-1/8
+
+ x<-sapply(degrees,FUN=sin)*s + 0.5
+ y<-sapply(degrees,FUN=cos)*s + 0.5
+
+
+ if(!require(grid)) {
+ stop("Need access to 'grid' library.")
+ }
+ grid.newpage()
+ grid.circle(x,y,3/12,name="some name")
+
+ ##cat("filling data\n")
+
+ distFromZero<-rep(NA,2^numCircles)
+ degrees<-rep(NA,2^numCircles)
+
+ degrees[(2^numCircles)]<-0
+ distFromZero[(2^numCircles)]<-0
+
+ for (i in 0:(numCircles-1)) {
+ distFromZero[2^i+1] <- 4/12
+ degrees[2^i+1] <- 2*pi/numCircles*i
+ d<-degrees[2^i+1]
+
+ #print(data.colnames)
+
+ grid.text(
+ # starting from the lowest bit, hence reading
+ # lables from the right
+ label=data.colnames[numCircles - i],
+ x=sin(d)*5/12+0.5,
+ y=cos(d)*5/12+0.5,
+ rot=0
+ )
+
+ }
+
+ if (4==numCircles) {
+ for (i in 0:(numCircles-1)) {
+ # Current set bit plus the bit left of it and the bit right of it
+ distFromZero[2^i
+ +2^((i+numCircles-1)%%numCircles)
+ +2^((i+1)%%numCircles)+1] <- 2/12
+ degrees[2^i
+ +2^((i+numCircles-1)%%numCircles)
+ +2^((i+1)%%numCircles)+1] <- degrees[2^i+1]
+ }
+ }
+
+ #degrees[2^i+1] + degrees[2^((i+1)%%numCircles)+1])/2
+
+ if (3 <=numCircles) {
+ for (i in 0:(numCircles-1)) {
+ distFromZero[(2^i+2^((i+1)%%numCircles))+1]<- 3/12
+ if (i == (numCircles-1)) {
+ degrees[(2^i+2^((i+1)%%numCircles))+1] <- (
+ degrees[2^i+1] + 2*pi+ degrees[1+1])/2
+ }
+ else {
+ degrees[(2^i+2^((i+1)%%numCircles))+1] <- (
+ degrees[2^i+1] + degrees[2^((i+1)%%numCircles)+1])/2
+ }
+
+ }
+ }
+
+ for(i in 1:2^numCircles) {
+ n<-paste(baseOf((i-1),2,numCircles),collapse="")
+ v<-data[n,1]
+ d<-degrees[i]
+ if (1 == length(d) && is.na(d)) {
+ if (v>0) warning("Not shown: ",n,"is",v,"\n")
+ }
+ else {
+ l<-distFromZero[i]
+ x<-sin(d)*l+0.5
+ y<-cos(d)*l+0.5
+ #cat("i=",i," x=",x," y=",y," label=",n,"\n")
+ l<-v
+ if (showSetLogicLabel) l<-paste(n,"\n",v,sep="")
+ grid.text(label=l,x=x,y=y,rot=0)
+ }
+ }
+ }
+ else if (4 <= numCircles && numCircles <= 5 && !simplify) {
+
+ grid.newpage()
+ # Function to turn and move ellipses
+ relocate_elp <- function(e, alpha, x, y){
+ phi=(alpha/180)*pi;
+ xr=e[,1]*cos(phi)+e[,2]*sin(phi)
+ yr=-e[,1]*sin(phi)+e[,2]*cos(phi)
+ xr=x+xr;
+ yr=y+yr;
+ return(cbind(xr, yr))
+ }
+
+ lab<-function (identifier, data, showLabel=showSetLogicLabel) {
+ r<-data[identifier,1]
+ if (showLabel) {
+ return(paste(identifier,r,sep="\n"))
+ }
+ else {
+ return(r)
+ }
+ }
+
+ plot(c(0, 400), c(0, 400), type="n", axes=F, ylab="", xlab="")
+ if (4 == numCircles) {
+ elps=cbind(162*cos(seq(0,2*pi,len=1000)), 108*sin(seq(0,2*pi,len=1000)));
+
+ plot(c(0, 400), c(0, 400), type="n", axes=F, ylab="", xlab="");
+ polygon(relocate_elp(elps, 45,130, 170));
+ polygon(relocate_elp(elps, 45,200, 200));
+ polygon(relocate_elp(elps, 135,200, 200));
+ polygon(relocate_elp(elps, 135,270, 170));
+
+ text( 35, 315, data.colnames[1],cex=1.5)
+ text(138, 347, data.colnames[2],cex=1.5)
+ text(262, 347, data.colnames[3],cex=1.5)
+ text(365, 315, data.colnames[4],cex=1.5)
+
+ elps <- cbind(130*cos(seq(0,2*pi,len=1000)),
+ 80*sin(seq(0,2*pi,len=1000)))
+
+ text( 35, 250, lab("1000",data));
+ text(140, 315, lab("0100",data));
+ text(260, 315, lab("0010",data));
+ text(365, 250, lab("0001",data));
+
+ text( 90, 280, lab("1100",data), cex=small)
+ text( 95, 110,lab("1010",data) )
+ text(200, 50, lab("1001",data), cex=small)
+ text(200, 290, lab("0110",data))
+ text(300, 110, lab("0101",data))
+ text(310, 280, lab("0011",data), cex=small)
+
+ text(130, 230, lab("1110",data))
+ text(245, 75, lab("1101",data),cex=small)
+ text(155, 75, lab("1011",data),cex=small)
+ text(270, 230, lab("0111",data))
+
+ text(200,150,lab("1111",data))
+ }
+ else if (5 == numCircles) {
+
+ elps <- cbind(150*cos(seq(0,2*pi,len=1000)),
+ 60*sin(seq(0,2*pi,len=1000)))
+
+ polygon(relocate_elp(elps, 90,200, 250))
+ polygon(relocate_elp(elps, 162,250, 220))
+ polygon(relocate_elp(elps, 234,250, 150))
+ polygon(relocate_elp(elps, 306,180, 125))
+ polygon(relocate_elp(elps, 378,145, 200))
+
+ text( 50, 280, data.colnames[1],cex=1.5)
+ text(150, 400, data.colnames[2],cex=1.5)
+ text(350, 300, data.colnames[3],cex=1.5)
+ text(350, 20, data.colnames[4],cex=1.5)
+ text( 50, 10, data.colnames[5],cex=1.5)
+
+ text( 61, 228, lab("10000",data));
+ text(194, 329, lab("01000",data));
+ text(321, 245, lab("00100",data));
+ text(290, 81, lab("00010",data));
+ text(132, 69, lab("00001",data));
+
+ text(146, 250, lab("11000",data), cex=small)
+ text(123, 188, lab("10100",data), cex=small)
+ text(275, 152, lab("10010",data), cex=small)
+ text(137, 146, lab("10001",data), cex=small)
+ text(243, 268, lab("01100",data), cex=small)
+ text(175, 267, lab("01010",data), cex=small)
+ text(187, 117, lab("01001",data), cex=small)
+ text(286, 188, lab("00110",data), cex=small)
+ text(267, 235, lab("00101",data), cex=small)
+ text(228, 105, lab("00011",data), cex=small)
+
+ text(148, 210, lab("11100",data),cex=small)
+ text(159, 253, lab("11010",data),cex=small)
+ text(171, 141, lab("11001",data),cex=small)
+ text(281, 175, lab("10110",data),cex=small)
+ text(143, 163, lab("10101",data),cex=small)
+ text(252, 145, lab("10011",data),cex=small)
+ text(205, 255, lab("01110",data),cex=small)
+ text(254, 243, lab("01101",data),cex=small)
+ text(211, 118, lab("01011",data),cex=small)
+ text(267, 211, lab("00111",data),cex=small)
+
+ text(170, 231,lab("11110",data),cex=small)
+ text(158, 169,lab("11101",data),cex=small)
+ text(212, 139,lab("11011",data),cex=small)
+ text(263, 180,lab("10111",data),cex=small)
+ text(239, 232,lab("01111",data),cex=small)
+
+ text(204,190,lab("11111",data))
+ }
+ }
+ else {
+ stop(paste("The printing of ",numCircles," circles is not yet supported."))
+ }
+
+}
+
+
+venn <- function(data,
+ universe=NA,
+ small=0.7,
+ showSetLogicLabel=FALSE,
+ simplify=FALSE,
+ show.plot=TRUE)
+{
+ counts <- getVennCounts(data)
+
+ if(show.plot)
+ drawVennDiagram(data=counts,
+ small=small,
+ showSetLogicLabel=showSetLogicLabel,
+ simplify=simplify
+ )
+
+ invisible(counts)
+}
Added: trunk/gplots/man/venn.Rd
===================================================================
--- trunk/gplots/man/venn.Rd (rev 0)
+++ trunk/gplots/man/venn.Rd 2008-05-20 00:14:51 UTC (rev 1271)
@@ -0,0 +1,78 @@
+\name{venn}
+\alias{venn}
+\title{Plot a Venn diagram}
+\description{
+Plot Venn diagrams for up to 5 sets
+}
+\usage{
+venn(data, small = 0.7, showSetLogicLabel = FALSE, simplify = FALSE)
+}
+\arguments{
+ \item{data}{data to be plotted (see below)}
+ \item{small}{Character size of group labels}
+ \item{showSetLogicLabel}{Logical flag indicating whether the internal
+ group label should be displayed}
+ \item{simplify}{Logical flag indicating whether unobserved group
+ should be omitted.}
+}
+\details{
+ \code{data} should be either a named list of vectors containing
+ indexes of group members (1, 2, 3,..) , or a data frame containing indicator
+ variables (TRUE, FALSE, TRUE, ..) for group membership. Group names
+ will be taken from the component vector or column names.
+}
+\value{
+ A matrix of all possible sets of groups, and the observed numer of
+ items beloinging to each set of groups is returned invisibly.
+ The fist column contains observed counts, subsequent columns contain
+ 0-1 indicators of group membership.
+}
+\author{Steffen Moeller \email{ste...@gm...},
+ with cleanup and packaging by Gregory R. Warnes
+ \email{gr...@ra...}.}
+\examples{
+
+##
+## Example using a list of item indexes belonging to the
+## specified group.
+##
+A<- 1:20
+B<- 1:20
+C<- 2:20
+D<- 3:21
+input<-list(A,B,C,D)
+input
+
+venn(input)
+
+##
+## Example using a data frame of indicator columns
+##
+A<- as.logical(rbinom(100, 1, 0.2))
+B<- as.logical(rbinom(100, 1, 0.7))
+C<- as.logical(rbinom(100, 1, 0.2))
+D<- as.logical(rbinom(100, 1, 0.1))
+input<-data.frame(A,B,C,D)
+venn(input)
+
+
+## Omit un-observed groupings
+tmp <- venn(input, simplify=T)
+
+## show details
+tmp
+
+## Show internal binary group labels
+venn(input, showSetLogicLabel=TRUE)
+
+## Omit un-observed groupings, and show internal binary group labels
+venn(input, simplify=T, showSetLogicLabel=TRUE)
+
+
+
+
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ ~kwd1 }
+\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line
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|
|
From: <wa...@us...> - 2008-05-20 01:07:33
|
Revision: 1272
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1272&view=rev
Author: warnes
Date: 2008-05-19 18:07:28 -0700 (Mon, 19 May 2008)
Log Message:
-----------
Fix code/doc mismatch due to recent changes to bandplot()
Modified Paths:
--------------
trunk/gplots/R/bandplot.R
trunk/gplots/man/bandplot.Rd
Modified: trunk/gplots/R/bandplot.R
===================================================================
--- trunk/gplots/R/bandplot.R 2008-05-20 00:14:51 UTC (rev 1271)
+++ trunk/gplots/R/bandplot.R 2008-05-20 01:07:28 UTC (rev 1272)
@@ -9,7 +9,6 @@
sd.lwd=c(2,2,3,2,2),
sd.lty=c(2,1,1,1,2),
method="frac", width=1/5,
- use.runsd=TRUE,
n=50
)
{
Modified: trunk/gplots/man/bandplot.Rd
===================================================================
--- trunk/gplots/man/bandplot.Rd 2008-05-20 00:14:51 UTC (rev 1271)
+++ trunk/gplots/man/bandplot.Rd 2008-05-20 01:07:28 UTC (rev 1272)
@@ -28,8 +28,8 @@
}
\usage{
bandplot(x, y, ..., add = FALSE, sd = c(-2:2),
- sd.col = c("lightblue", "blue", "red", "blue", "lightblue"),
- sd.lwd = c(1, 2, 3, 2, 1), sd.lty = c(2, 1, 1, 1, 2),
+ sd.col=c("magenta", "blue", "red", "blue", "magenta"),
+ sd.lwd=c(2, 2, 3, 2, 2), sd.lty=c(2, 1, 1, 1, 2),
method = "frac", width = 1/5, n=50)
}
\arguments{
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|
|
From: <wa...@us...> - 2008-05-20 01:13:23
|
Revision: 1274
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1274&view=rev
Author: warnes
Date: 2008-05-19 18:13:18 -0700 (Mon, 19 May 2008)
Log Message:
-----------
Update man page to match recent changes to plot.lm2()
Modified Paths:
--------------
trunk/gplots/DESCRIPTION
trunk/gplots/man/plot.lm2.Rd
Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION 2008-05-20 01:08:55 UTC (rev 1273)
+++ trunk/gplots/DESCRIPTION 2008-05-20 01:13:18 UTC (rev 1274)
@@ -1,9 +1,9 @@
Package: gplots
Title: Various R programming tools for plotting data
Description: Various R programming tools for plotting data
-Depends: R (>= 1.9.0), gtools, gdata, stats, caTools
+Depends: R (>= 1.9.0), gtools, gdata, stats, caTools, grid
Recommends: datasets, grid
-Suggests: gtools, grid
+Suggests: gtools
Version: 2.7.0
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by (in alphabetical order):
Modified: trunk/gplots/man/plot.lm2.Rd
===================================================================
--- trunk/gplots/man/plot.lm2.Rd 2008-05-20 01:08:55 UTC (rev 1273)
+++ trunk/gplots/man/plot.lm2.Rd 2008-05-20 01:13:18 UTC (rev 1274)
@@ -7,14 +7,25 @@
Plots to assess the goodness of fit for the linear model objects
}
\usage{
- plot.lm2(x, which = 1:5, caption = c("Residuals vs Fitted",
- "Normal Q-Q plot", "Scale-Location plot",
- "Cook's distance plot"), panel = panel.smooth,
- sub.caption = deparse(x$call), main = "",
- ask = interactive() && nb.fig < length(which)
- && .Device != "postscript", ..., id.n = 3,
- labels.id = names(residuals(x)),
- cex.id = 0.75, band = TRUE, rug = TRUE)
+ plot.lm2(
+ x,
+ which = 1:5,
+ caption = c("Residuals vs Fitted", "Normal Q-Q plot",
+ "Scale-Location plot", "Cook's distance plot"),
+ panel = panel.smooth,
+ sub.caption = deparse(x$call),
+ main = "",
+ ask = interactive() && nb.fig < length(which)
+ && .Device != "postscript",
+ ...,
+ id.n = 3,
+ labels.id = names(residuals(x)),
+ cex.id = 0.75,
+ band=TRUE,
+ rug=TRUE,
+ width=1/10,
+ max.n=5000
+ )
}
\arguments{
\item{x}{lm object}
@@ -39,16 +50,22 @@
\item{band}{logical vector indicating whether bandplot should also be plotted }
\item{rug}{logical vector indicating whether rug should be added to
the existing plot }
+ \item{width}{Fraction of the data to use for plot smooths}
+ \item{max.n}{Maximum number of points to display in plots}
}
\author{Gregory R. Warnes \email{wa...@bs...} and Nitin
Jain \email{nit...@pf...}}
\examples{
- ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
- trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
- group <- gl(2,10,20, labels=c("Ctl","Trt"))
- weight <- c(ctl, trt)
- x <- lm(weight ~ group)
- plot.lm2(x, which=1)
-plot.lm2(x, which=1:3)
+ctl <- rnorm(100, 4)
+trt <- rnorm(100, 4.5)
+group <- gl(2,100,200, labels=c("Ctl","Trt"))
+weight <- c(ctl, trt)
+wt.err <- rnorm(length(weight), mean=weight, sd=1/2)
+x <- lm(weight ~ group + wt.err)
+
+plot.lm2(x)
+
+plot.lm2(x, which=1, width=1/3)
+plot.lm2(x, which=1:3, widht=1/3)
}
\keyword{hplot}
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|
|
From: <wa...@us...> - 2008-06-16 14:18:51
|
Revision: 1296
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1296&view=rev
Author: warnes
Date: 2008-06-16 07:18:50 -0700 (Mon, 16 Jun 2008)
Log Message:
-----------
Add TODO list to gplots
Added Paths:
-----------
trunk/gplots/TODO
trunk/gplots/inst/TODO
Added: trunk/gplots/TODO
===================================================================
--- trunk/gplots/TODO (rev 0)
+++ trunk/gplots/TODO 2008-06-16 14:18:50 UTC (rev 1296)
@@ -0,0 +1 @@
+link inst/TODO
\ No newline at end of file
Property changes on: trunk/gplots/TODO
___________________________________________________________________
Name: svn:special
+ *
Added: trunk/gplots/inst/TODO
===================================================================
--- trunk/gplots/inst/TODO (rev 0)
+++ trunk/gplots/inst/TODO 2008-06-16 14:18:50 UTC (rev 1296)
@@ -0,0 +1,10 @@
+
+plot.lm2
+--------
+
+- Upgrade to match current plot.lm code
+- For predictor vs resid, use boxplot when predictor is a factor
+- Rug plot or histogram for residuals/fitted values in both dimensions
+- Confidence region for normal distribution with equivalent number of points on QQ plot
+- display "bad" cutoff line for cook's distance plot
+
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