NEWS.md
Major change:
Bug Fixes:
Misc
Bug Fixes:
An error in plotLowess() prevented it from finding objects in the caller’s environment.
The manual page for heatmap.2() stated the incorrect type for the ‘layout’ element of the return list. It is a named list, not a named numeric vector.
New Features:
New angleAxis() function to create axis labels with rotated text.
Bug Fixes:
Defunct message for boxplot.n() was recommending the wrong function.
Other Changes:
New Features:
heatmap.2() has two new arguments, ‘colRow’ and ‘colCol’ to control the color of row and column text labels. See the man page for examples.
heatmap.2() has been modified to make it easier to extract and plot subclusters from a large heatmap. Simply pass the dendrogram of the subcluster together with the full data matrix and, optionally, the breaks of the full heatmap in order to obtain the same color scaling. (Suggestion and patch contributed by Ilia Kats.)
venn() now returns a list of the members of each set intersection in the attribute ‘intersections’. This can be disabled using the argument ‘intersection=FALSE’ (Patch by Steffen Möller.)
Bug Fixes:
In heatmap.2(), the color key now properly handles color breaks that are not equally spaced. (Issue reported by Tim Richter-Heitmann.)
In heatmap.2(), row/column traces in could be plotted on the wrong row/column.
plotCI() now properly respects the ‘type=’ argument. (Bug report and correction by Wiktor Żelazny.)
Remove stray browser() call from overplot()
In the balloonplot() examples, explicitly specify the ‘neworder’ argument to gplots:::reorder.factor to prevent errors.
Other Changes:
smartlegend() is now deprecated because the relative positioning feature (‘top’, ‘right’) has been added to graphics::legend(). Calling smartlegend() will generate a warning.
boxplot.n() and plot.lm2() are defunct have been removed. Use of these functions will now generate an error.
Update out-of-date URLs in man pages.
New Features:
Bug Fixes:
New features:
Other changes:
Bug Fixes:
heatmap.2() was not respecting key.title=NA when density.info=“none”.
Correct the man page for heatmap.2 to state that the default color for ‘notecol’ is cyan.
In heatmap.2(), modify default arguments to ‘symbreaks’ and ‘symkey’ to make the logic more evident by replacing min(…) with any(…). (The previous code executed properly, but relied on implicit coercion of logicals to numeric, obscuring the intent.)
Calling heatmap.2 with deeply nested dendrograms could trigger a ‘node stack overflow’ error. Now, this situation is deteceted, and a message is generated indicating how to increase the relevant recursion limit via options(“expressions”=…).
Bug Fixes:
Bug Fixes:
Enhancements:
heatmap.2(): Add new ‘reorderfun’ argument to allow the user to specify an alternative function to reorder rows/columns based on row/column dendrogram. (Suggested by Yuanhua Liu.)
heatmap.2(): Center margin labels.
heatmap.2(): Check size of user-provided Rowv and Colv dendrogram objects to ensure they match the dimensions of the data.
Add references to man page for hist2d() and ci2d() to the new r2d2 package which implements an improved algorithm for 2-dimensional emprical confidence regions.
Bug Fixes:
Enhancements:
In heatmap.2, when the row or column trace is enabled, show the corresponding reference line in the color key.
In heatmap.2, a new ‘extrafun’ argument is provided that allows the user to specify a function to be called before the function returns. This allows the user to add additional plots to the page.
API Changes:
boxplot.n() has been renamed to boxplot2() to avoid potential S3 method calling issues.
plot.lm2() has been rename to lmplot2() to avoid potential S3 method calling issues.
Enhancements:
Bug Fixes:
Fix error in in venn() when all groups contained the same number of TRUE cases.
Correct error in overplot() when that occured when a group-category contained no finite values.
Other Changes:
Changes to overplot() to avoid warnings from upcoming enhancements to R CMD check.
Move several packages from Depends to Imports or Suggests.
Packages caTools and KernSmooth now have namespaces, so import needed functions in NAMESPACE.
Mark one example in manual page for ci2d ‘dontrun’ to avoid timing warning in R CMD check.
Enhancements:
Bug Fixes:
Enhancements:
Bug Fixes:
Updates:
New Features:
Objects returned by hist2d() have been changed: 1) $x and $y now contain the n midpoints of the bins in each direction 2) $x.breaks, $y.breaks now contain the n+1 limits of the bins in each direction.
Add lwd argument to plotmeans().
Bug Fixes:
Correct error in handling binning in hist2d(): (N+1)x(N+1) bins were being created instead of NxN bins, and the highest row/column in each direction was being omitted from the results and plot.
Changes to fix R CMD check warnings
New features:
New Features:
New ci2d() function to create 2-dimensional empirical confidence intervals utilizing KernSmooth:bkde2D and gplots::hist2d(). See ?ci2d for details.
Add ‘alpha’ argument to rich.colors() to control transparency.
Improvements:
Bug Fixes:
Improvements:
venn() now returns an object of class venn() and a plot method for this class is provided.
Manual page for venn has been improved, based on contributions by Steffen Moeller
Improvements:
Bug Fixes:
Bug Fixes:
Bug Fixes:
New Features:
Enhancements to heatmap.2()
New arguments ‘lmat’, ‘lhei’, and ‘lwid’ that allow controlling component plot layout. Users can now resize and rearrange plot components.
heatmap.2() will now compute color breakpoints that are symmetric about 0 when the new ‘symbreak’ parameter is TRUE. This parameter, as well as the symkey parameter now default to TRUE whenever negative values of x are present, and to FALSE othewise.
the heatmap.2() return value now includes additional useful information, including: call, rowMeans, rowSDs, colMeans, colSDs, carpet (reordered and scaled ‘x’ values), rowDendrogram, colDendrogram, breaks, col, vline, hline, and colorTable. Of these, the most useful are breaks, col, and colorTable. The latter is a three-column data frame providing the lower and upper bound and color for each bin.
See the manual page for complete details and examples.
New function venn(), contributed by Steffen Moeller (Thanks Steffen!) to generate Venn diagrams for up to 5 sets. See ?venn for details.
Performance of bandplot() has been dramatically improved, in part by using runsd() and runmean() from the caTools package. As a consequence, gplots now depends on the caTools package.
Improved performance of gplots::plot.lm for large lm objects by using the new bandplot() and by using fitted() instead of predict() to obtain y-hat.
Add ‘scale.range’ argument to balloonplot(), option to scale balloons so [min,max]->[0,1] (‘relative’) or [0,max] -> [0,1] (‘absolute’).
Bug Fixes:
balloonplot() now properly handles dimension labels provided by ‘xlab’ and ‘ylab’
plotCI now properly handles ‘NULL’ and ‘NA’ values for ui, li, uiw, and liw.
Corrections of minor typos in man pages
Update Greg’s email address to ‘greg@random-technologies-llc.com’
New Features:
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
New Features:
textplot() now converts tab characters to spaces before processing to avoid problems with computing height and width of text that includes tabs.
Add col2hex() function to convert color names to rgb hex codes
Bug Fixes:
Correct balloonplot.default to properly show specified x and y axis labels when explicitly provided
R/balloonplot.R: Correct error in balloonplot when z contains NA values.
Fix typos and code/doc mismatches identified by the latest R CMD check
Other:
New Features:
Add parameters to bandplot() to control line width and type.
Add paramaeters to textplot.matrix() to allow specification of the color of the matrix data, rows, and column
Bug Fixes:
Other:
Changed maintainer back to Greg Warnes
Updated Greg’s email address
heatmap.2.R: Fixed a bug which displayed warnings when Rowv and Colv were specified as dendrograms
plotmeans.R: Fixed bug in plotmeans - based on Stefano Calza’s suggestion (the function didn’t account for factors unused levels, returning an error.)
exported plot.lm to NAMESPACE, Remove .Alias calls in plot.lm.R since .Alias is defunct.
barplot2.R: Changed the default grey colors to heat colors, if height is matrix
Updated Greg’s email address
balloonplot.R: Recent changes to align row totals with the overall total broke how the marginal cumulative fractions were displayed. Added example using Titanic data that exercises the multi-factor display. Added -.tex, .pdf files and figuers, and RNEWS article in inst/doc
colorpanel.R: colorpanel now allows only 2 colors to be specified if no ‘middle’ color is desired.