579 lines
16 KiB
Plaintext
579 lines
16 KiB
Plaintext
Release 3.0.1 - 2016-03-30
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--------------------------
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Bug Fixes:
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- An error in plotLowess() prevented it from finding objects in
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the caller's environment.
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- The manual page for heatmap.2() stated the incorrect type for
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the 'layout' element of the return list. It is a named list,
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not a named numeric vector.
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Release 3.0.0 - 2016-03-28
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---------------------------
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New Features:
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- venn():
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- now support matrices of indicator values. Previously indicator
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values were only supported when supplied as a dataframe.
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- The 'intersections' attribute returned from venn() has been
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improved so that goups are labeled using set names instead
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of indicators, and are ordered from simplest to most complex
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set intersection.
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- New angleAxis() function to create axis labels with rotated text.
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- heatmap.2():
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- heatmap.2() can now be used to plot subsets of a previous
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heatmap.
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- Decrease the granularity of the carpet in heatmap.2()'s
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color key to avoid visual artifacts.
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- Returned object now includes 'layout' element that contains
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layout information. (Patch provided by Jenny Drnevich.)
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- lowess():
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- New function plotLowess() to display a scatter plot with a
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superimposed lowess curve.
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- The lowess() functions now returns a list object of class
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'lowess'
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- A new lowess method for plot() method for 'lowess' objects
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that generates a scatterplot of the raw data with a lowess
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curve superimposed.
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Bug Fixes:
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- Defunct message for boxplot.n() was recommending the wrong
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function.
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- heatmap.2():
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- Remove debugging print() statement.
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- Now properly sets 'srtCol' default if missing and 'colCol' is
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specified.
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- Corrected a bug causing "Error in plot.new() : figure margins
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too large" to occur when 'key=FALSE'. (Reported and patch
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provided by Sveinung Gundersen.)
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- Corrected a bug causing an error when "Rowv=FALSE" or "Colv=FALSE".
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- Corrected message when "Rowv=FALSE" or "Colv=FALSE" and the the
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"dendrogram" argument requested the corresponding dendrogram.
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- venn():
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- Fix warning message that was missing spaces between words.
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Other Changes:
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- The smartlegend(), plot.lm2(), and boxplot.n() functions are now
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defunct. Please use grephics::legend(), lmplot2() or boxplot2()
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respectively.
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Release 2.17.0 - 2015-05-01
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---------------------------
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New Features:
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- heatmap.2() has two new arguments, 'colRow' and 'colCol' to control
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the color of row and column text labels. See the man page for
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examples.
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- heatmap.2() has been modified to make it easier to extract and plot
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subclusters from a large heatmap. Simply pass the dendrogram of the
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subcluster together with the full data matrix and, optionally, the
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breaks of the full heatmap in order to obtain the same color
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scaling. (Suggestion and patch contributed by Ilia Kats.)
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- venn() now returns a list of the members of each set intersection in
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the attribute 'intersections'. This can be disabled using the
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argument 'intersection=FALSE' (Patch by Steffen Möller.)
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Bug Fixes:
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- In heatmap.2(), the color key now properly handles color breaks that
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are not equally spaced. (Issue reported by Tim Richter-Heitmann.)
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- In heatmap.2(), row/column traces in could be plotted on the wrong
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row/column.
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- plotCI() now properly respects the 'type=' argument. (Bug report
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and correction by Wiktor Żelazny.)
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- Remove stray browser() call from overplot()
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- In the balloonplot() examples, explicitly specify the 'neworder'
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argument to gplots:::reorder.factor to prevent errors.
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Other Changes:
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- smartlegend() is now deprecated because the relative positioning
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feature ('top', 'right') has been added to graphics::legend().
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Calling smartlegend() will generate a warning.
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- boxplot.n() and plot.lm2() are defunct have been removed. Use of
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these functions will now generate an error.
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- Update out-of-date URLs in man pages.
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Release 2.16.0 - 2015-01-02
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---------------------------
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New Features:
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- plotmeans() has a new argument, 'text.n.label' which specifies the
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text used for labeling the number of elements in a group.
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Bug Fixes:
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- plotmeans() now respects (optional) graphical arguments captured in
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'...' when drawing the x axis.
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Release 2.15.0 - 2014-12-01
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---------------------------
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New features:
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- Convert bandplot() to S3-method dispatch and add method for class
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formula, so that 'bandplot( y ~ x, data=dataframe )' now works as
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expected.
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Other changes:
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- heatmap.2() now uses a local *non-byte-compiled* copy of
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plot.dengrogram, because the byte-compiled stats:::plot.dendrogram
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uses a recursive algorithm that generates a 'node stack overflow'
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error for deeply nested dendrograms and the node stack size cannot
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be changed at execution time. Instead, tne local non-byte-compiled
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gplots:::plot.dendrogram will trigger a recursion limit for such
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dengrograms. heatmap.2() will detect this error and recommend that
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the user increase the recursion limit (via,
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e.g. 'options("expressions"=20000)' ) and rerun.
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Release 2.14.2 - 2014-09-17
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---------------------------
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Bug Fixes:
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- heatmap.2() was not respecting key.title=NA when density.info="none".
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- Correct the man page for heatmap.2 to state that the default color
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for 'notecol' is cyan.
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- In heatmap.2(), modify default arguments to 'symbreaks' and 'symkey'
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to make the logic more evident by replacing min(...) with
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any(...). (The previous code executed properly, but relied on
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implicit coercion of logicals to numeric, obscuring the intent.)
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- Calling heatmap.2 with deeply nested dendrograms could trigger a
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'node stack overflow' error. Now, this situation is deteceted, and
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a message is generated indicating how to increase the relevant
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recursion limit via options("expressions"=...).
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Release 2.14.1 - 2014-06-30
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---------------------------
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Bug Fixes:
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- Correct heatmap.2() bug in Colv dendrogram object dimension checking introduced
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in 2.14.0. (Reported by Yong Fuga Li.)
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Release 2.14.0 - 2014-06-18
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---------------------------
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Bug Fixes:
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- heatmap.2(): Fix typo in heatmap.2() that caused an error when
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'Rowv=FALSE'. (Reported by Yuanhua Liu.)
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Enhancements:
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- heatmap.2(): Add new 'reorderfun' argument to allow the user to
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specify an alternative function to reorder rows/columns based on
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row/column dendrogram. (Suggested by Yuanhua Liu.)
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- heatmap.2(): Center margin labels.
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- heatmap.2(): Check size of user-provided Rowv and Colv dendrogram
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objects to ensure they match the dimensions of the data.
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- Add references to man page for hist2d() and ci2d() to the new r2d2
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package which implements an improved algorithm for 2-dimensional
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emprical confidence regions.
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Release 2.13.0 - 2014-04-04
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---------------------------
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Bug Fixes:
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- heatmap.2 was not properly handling row trace reference line ('hline').
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Patch submitted by Ilia Kats.
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Enhancements:
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- In heatmap.2, when the row or column trace is enabled, show the
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corresponding reference line in the color key.
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- In heatmap.2, a new 'extrafun' argument is provided that allows the
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user to specify a function to be called before the function returns.
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This allows the user to add additional plots to the page.
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Release 2.12.1 - 2013-10-14
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---------------------------
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API Changes:
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- boxplot.n() has been renamed to boxplot2() to avoid potential S3
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method calling issues.
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- plot.lm2() has been rename to lmplot2() to avoid potential S3 method
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calling issues.
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Enhancements:
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- Add heatmap.2() parameters to control row and column label rotation
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('srtRow', 'srtCol'), justification ('adjRow', 'adjCol'), and space
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from plot edge ('offsetRow', 'offsetCol').
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Bug Fixes:
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- Fix error in in venn() when all groups contained the same number of TRUE cases.
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- Correct error in overplot() when that occured when a group-category contained no
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finite values.
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Other Changes:
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- Changes to overplot() to avoid warnings from upcoming enhancements to R CMD check.
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- Move several packages from Depends to Imports or Suggests.
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- Packages caTools and KernSmooth now have namespaces, so import
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needed functions in NAMESPACE.
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- Mark one example in manual page for ci2d 'dontrun' to avoid timing
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warning in R CMD check.
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Release 2.11.3 - 2013-06-27
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---------------------------
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Enhancements:
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- Modify sinkplot() to use a local environment rather than the global
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environment, to conform to CRAN policies.
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Bug Fixes:
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- Fixed typo/spelling error in plotmeans() man page.
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Release 2.11.2 - 2013-03-24
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---------------------------
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Enhancements:
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- Add ci.width argument to barplot2() to allow varying the length of
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the 't' at the end of confidence interval bars.
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Bug Fixes:
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- Fix error in heatmap.2 when colsep argument had length 1.
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Updates:
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- Update manual page for lowess.default() to
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match changed argument list for lowess() in R 3.0.0
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Release 2.11.1 - 2012-12-14
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---------------------------
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Bug Fixes:
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- Replace corrupted BalloonPlot.pdf in inst/doc.
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Release 2.11.0 - 2012-06-08
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---------------------------
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New Features:
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- Objects returned by hist2d() have been changed:
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1) $x and $y now contain the n midpoints of the bins in each direction
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2) $x.breaks, $y.breaks now contain the n+1 limits of the bins in
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each direction.
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- Add lwd argument to plotmeans().
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Bug Fixes:
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- Correct error in handling binning in hist2d(): (N+1)x(N+1) bins were
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being created instead of NxN bins, and the highest row/column in
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each direction was being omitted from the results and plot.
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- Changes to fix R CMD check warnings
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Release 2.10.1 - 2011-09-02
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---------------------------
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New features:
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- Make results of hist2d() and ci2d() into objects, and add print()
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methods to display them.
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Release 2.10.0 - 2011-08-26
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---------------------------
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New Features:
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- New ci2d() function to create 2-dimensional empirical confidence
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intervals utilizing KernSmooth:bkde2D and gplots::hist2d().
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See ?ci2d for details.
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- Add 'alpha' argument to rich.colors() to control transparency.
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Improvements:
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- Accellerate hist2d by replacing for() loop with tapply(), and allow
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user to specify summary function applied (per suggestion by Peter
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Hagedorn).
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Bug Fixes:
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- Correct error in heatmap.2() that arises when data includes NA values
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(identified by Melissa Key).
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Release 2.8.0 - 2010-06-10
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--------------------------
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Improvements:
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- venn() now returns an object of class venn() and a plot method for
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this class is provided.
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- Manual page for venn has been improved, based on contributions by
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Steffen Moeller
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Release 2.7.5 - ??
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--------------------------
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Improvements:
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- Performance of 'hist2d' improved thanks to a suggestion from
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Joerg van den Hoff.
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Release 2.7.4 - 2009-11-12
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--------------------------
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Bug Fixes:
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- Correct bug reported by Alan Yong: plotmeans() failed when bars=FALSE.
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Release 2.7.3 - 2009-10-22
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--------------------------
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Bug Fixes:
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- Correct bug reported by Rudolf Talens: heatmap.2() incorrectly
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transposed the displayed matrix when the option symm=TRUE.
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Release 2.7.2 - 2009-05-08
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--------------------------
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Bug Fixes:
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- Correct bug reported by Ken Lo: cox2hex() had blue and green
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components swapped.
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Release 2.7.1 - 2009-05-08
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--------------------------
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New Features:
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- Enhancements to heatmap.2()
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- New arguments 'lmat', 'lhei', and 'lwid' that allow controlling
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component plot layout. Users can now resize and rearrange plot
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components.
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- heatmap.2() will now compute color breakpoints that are
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symmetric about 0 when the new 'symbreak' parameter is TRUE. This
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parameter, as well as the symkey parameter now default to TRUE
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whenever negative values of x are present, and to FALSE othewise.
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- the heatmap.2() return value now includes additional useful
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information, including: call, rowMeans, rowSDs, colMeans,
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colSDs, carpet (reordered and scaled 'x' values), rowDendrogram,
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colDendrogram, breaks, col, vline, hline, and colorTable. Of
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these, the most useful are breaks, col, and colorTable. The
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latter is a three-column data frame providing the lower and
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upper bound and color for each bin.
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See the manual page for complete details and examples.
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- New function venn(), contributed by Steffen Moeller (Thanks
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Steffen!) to generate Venn diagrams for up to 5 sets. See ?venn for
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details.
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- Performance of bandplot() has been dramatically improved, in part by
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using runsd() and runmean() from the caTools package. As a
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consequence, gplots now depends on the caTools package.
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- Improved performance of gplots::plot.lm for large lm objects by
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using the new bandplot() and by using fitted() instead of predict()
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to obtain y-hat.
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- Add 'scale.range' argument to balloonplot(), option to scale
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balloons so [min,max]->[0,1] ('relative') or [0,max] -> [0,1]
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('absolute').
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Bug Fixes:
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- balloonplot() now properly handles dimension labels provided by
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'xlab' and 'ylab'
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- plotCI now properly handles 'NULL' and 'NA' values for ui, li, uiw,
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and liw.
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- Corrections of minor typos in man pages
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- Update Greg's email address to 'greg@random-technologies-llc.com'
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Release 2.6.0 - 2008-04-07
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--------------------------
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New Features:
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- heatmap() now allows control of the location of individual plot components
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(e.g. color key)
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Bug Fixes:
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- Fix bug in handling rowsep, per suggestion by Steven Paugh
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- Fix examples for overplot()
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- Two letter clarification of help text for heatmap.2()
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- Restore plot layout settings to default state at end of ooplot() example
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- Various typo fixes
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Release 2.5.0 - 2007-11-02
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--------------------------
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New Features:
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- textplot() now converts tab characters to spaces before processing to
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avoid problems with computing height and width of text that includes
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tabs.
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- Add col2hex() function to convert color names to rgb hex codes
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Bug Fixes:
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- Correct balloonplot.default to properly show specified x and y axis
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labels when explicitly provided
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- R/balloonplot.R: Correct error in balloonplot when z contains NA values.
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- Fix typos and code/doc mismatches identified by the latest R CMD check
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Other:
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- Clarify GPL version
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Release 2.4.0 - 2007-02-08
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--------------------------
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New Features:
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- Add parameters to bandplot() to control line width and type.
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- Add paramaeters to textplot.matrix() to allow specification of the
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color of the matrix data, rows, and column
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Bug Fixes:
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Other:
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Release 2.3.2 - 2006-11-14
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--------------------------
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- heatmap.2.Rd: Fix example that was broken by changes in 2.3.0.
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Release 2.3.1
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-------------
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- Changed maintainer back to Greg Warnes
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- Updated Greg's email address
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- heatmap.2.R: Fixed a bug which displayed warnings when Rowv and Colv
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were specified as dendrograms
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Release 2.3.0
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-------------
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- heatmap.2.R, heatmap.2.Rd:
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Updated the code and man page to make sure the Rowv and Colv
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values are properly handled
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- Added the tests directory
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Release 2.2.0
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-------------
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- plotmeans.R: Fixed bug in plotmeans - based on Stefano Calza's
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suggestion (the function didn't account for factors
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unused levels, returning an error.)
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- exported plot.lm to NAMESPACE, Remove .Alias calls in plot.lm.R
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since .Alias is defunct.
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- barplot2.R: Changed the default grey colors to heat colors, if
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height is matrix
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- Updated Greg's email address
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- balloonplot.R: Recent changes to align row totals with the
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overall total broke how the marginal cumulative
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fractions were displayed. Added example using
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Titanic data that exercises the multi-factor display.
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Added -.tex, .pdf files and figuers, and RNEWS article
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in inst/doc
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- colorpanel.R: colorpanel now allows only 2 colors to be specified
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if no 'middle' color is desired.
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Release 2.0.8
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-------------
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- Added DESCRIPTION and removed DESCRIPTION.in
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- Updated barplot2
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- Updated heatmap.2
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