[R-gregmisc-users] SF.net SVN: r-gregmisc:[1557] trunk/gplots
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[R-gregmisc-users] SF.net SVN: r-gregmisc:[1557] trunk/gplots
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From: <wa...@us...> - 2012-06-08 17:56:44
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Revision: 1557
http://r-gregmisc.svn.sourceforge.net/r-gregmisc/?rev=1557&view=rev
Author: warnes
Date: 2012-06-08 17:56:37 +0000 (Fri, 08 Jun 2012)
Log Message:
-----------
Fix R CMD check warnings.
Modified Paths:
--------------
trunk/gplots/DESCRIPTION
trunk/gplots/R/barplot2.R
trunk/gplots/R/ooplot.R
trunk/gplots/R/plotCI.R
trunk/gplots/R/sinkplot.R
trunk/gplots/man/qqnorm.aov.Rd
trunk/gplots/tests/heatmap2Test.Rout.save
Modified: trunk/gplots/DESCRIPTION
===================================================================
--- trunk/gplots/DESCRIPTION 2012-06-08 17:49:30 UTC (rev 1556)
+++ trunk/gplots/DESCRIPTION 2012-06-08 17:56:37 UTC (rev 1557)
@@ -1,11 +1,11 @@
Package: gplots
Title: Various R programming tools for plotting data
Description: Various R programming tools for plotting data
-Depends: R (>= 2.10), gtools, gdata, stats, caTools, grid, KernSmooth
-Recommends: datasets, grid, MASS
+Depends: R (>= 2.10), gtools, gdata, stats, caTools, grid, KernSmooth, MASS, datasets
+Recommends: grid
Suggests: gtools
-Version: 2.10.1
-Date: 2011-09-01
+Version: 2.11.0
+Date: 2012-06-08
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by (in alphabetical order):
Ben Bolker, Lodewijk Bonebakker, Robert Gentleman, Wolfgang
Modified: trunk/gplots/R/barplot2.R
===================================================================
--- trunk/gplots/R/barplot2.R 2012-06-08 17:49:30 UTC (rev 1556)
+++ trunk/gplots/R/barplot2.R 2012-06-08 17:56:37 UTC (rev 1557)
@@ -233,7 +233,7 @@
}
if (beside)
- w.m <- matrix(w.m, nc = NC)
+ w.m <- matrix(w.m, ncol = NC)
if(plot) ##-------- Plotting :
{
Modified: trunk/gplots/R/ooplot.R
===================================================================
--- trunk/gplots/R/ooplot.R 2012-06-08 17:49:30 UTC (rev 1556)
+++ trunk/gplots/R/ooplot.R 2012-06-08 17:56:37 UTC (rev 1557)
@@ -313,7 +313,7 @@
}
if (beside)
- w.m <- matrix(w.m, nc=NC)
+ w.m <- matrix(w.m, ncol=NC)
## check height/ci.l if using log scale to prevent log(<=0) error
## adjust appropriate ranges and bar base values
Modified: trunk/gplots/R/plotCI.R
===================================================================
--- trunk/gplots/R/plotCI.R 2012-06-08 17:49:30 UTC (rev 1556)
+++ trunk/gplots/R/plotCI.R 2012-06-08 17:56:37 UTC (rev 1557)
@@ -111,18 +111,6 @@
text(x, y, label=labels, col=col, ... )
}
}
- if(is.R())
- myarrows <- function(...) arrows(...)
- else
- myarrows <- function(x1,y1,x2,y2,angle,code,length,...)
- {
- segments(x1,y1,x2,y2,open=TRUE,...)
- if(code==1)
- segments(x1-length/2,y1,x1+length/2,y1,...)
- else
- segments(x2-length/2,y2,x2+length/2,y2,...)
- }
-
if(err=="y")
{
if(gap!=FALSE)
@@ -132,11 +120,11 @@
# draw upper bar
if(!is.null(li))
- myarrows(x , li, x, pmax(y-gap,li), col=barcol, lwd=lwd,
+ arrows(x , li, x, pmax(y-gap,li), col=barcol, lwd=lwd,
lty=lty, angle=90, length=smidge, code=1)
# draw lower bar
if(!is.null(ui))
- myarrows(x , ui, x, pmin(y+gap,ui), col=barcol,
+ arrows(x , ui, x, pmin(y+gap,ui), col=barcol,
lwd=lwd, lty=lty, angle=90, length=smidge, code=1)
}
else
@@ -147,10 +135,10 @@
# draw left bar
if(!is.null(li))
- myarrows(li, y, pmax(x-gap,li), y, col=barcol, lwd=lwd,
+ arrows(li, y, pmax(x-gap,li), y, col=barcol, lwd=lwd,
lty=lty, angle=90, length=smidge, code=1)
if(!is.null(ui))
- myarrows(ui, y, pmin(x+gap,ui), y, col=barcol, lwd=lwd,
+ arrows(ui, y, pmin(x+gap,ui), y, col=barcol, lwd=lwd,
lty=lty, angle=90, length=smidge, code=1)
}
Modified: trunk/gplots/R/sinkplot.R
===================================================================
--- trunk/gplots/R/sinkplot.R 2012-06-08 17:49:30 UTC (rev 1556)
+++ trunk/gplots/R/sinkplot.R 2012-06-08 17:56:37 UTC (rev 1557)
@@ -6,8 +6,8 @@
if( operation=="start" )
{
- if (exists(".sinkplot.conn", env=globalenv()) &&
- get(".sinkplot.conn", env=globalenv()) )
+ if (exists(".sinkplot.conn", envir=globalenv()) &&
+ get(".sinkplot.conn", envir=globalenv()) )
stop("sinkplot already in force")
@@ -20,22 +20,22 @@
}
else
{
- if (!exists(".sinkplot.conn", env=globalenv()) || !.sinkplot.conn )
+ if (!exists(".sinkplot.conn", envir=globalenv()) || !.sinkplot.conn )
stop("No sinkplot currently in force")
sink()
- data <- get(".sinkplot.data", env=globalenv())
+ data <- get(".sinkplot.data", envir=globalenv())
if( operation=="plot" )
textplot( paste( data, collapse="\n"), ... )
- close(get(".sinkplot.conn", env=globalenv()))
+ close(get(".sinkplot.conn", envir=globalenv()))
- if(exists(".sinkplot.data", env=globalenv()))
+ if(exists(".sinkplot.data", envir=globalenv()))
rm(".sinkplot.data", pos=globalenv())
- if(exists(".sinkplot.conn", env=globalenv()))
+ if(exists(".sinkplot.conn", envir=globalenv()))
rm(".sinkplot.conn", pos=globalenv())
invisible(data)
Modified: trunk/gplots/man/qqnorm.aov.Rd
===================================================================
--- trunk/gplots/man/qqnorm.aov.Rd 2012-06-08 17:49:30 UTC (rev 1556)
+++ trunk/gplots/man/qqnorm.aov.Rd 2012-06-08 17:56:37 UTC (rev 1557)
@@ -56,6 +56,8 @@
data(npk)
npk.aov <- aov(yield ~ block + N*P*K, npk)
qqnorm(npk.aov)
+
+## interactive labeling of points. Click mouse on points to show label.
if (dev.interactive()) qqnorm(npk.aov, omit=2:6, label=TRUE)
}
\keyword{ hplot }%
Modified: trunk/gplots/tests/heatmap2Test.Rout.save
===================================================================
--- trunk/gplots/tests/heatmap2Test.Rout.save 2012-06-08 17:49:30 UTC (rev 1556)
+++ trunk/gplots/tests/heatmap2Test.Rout.save 2012-06-08 17:56:37 UTC (rev 1557)
@@ -1,8 +1,8 @@
-R version 2.12.1 (2010-12-16)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R version 2.15.0 (2012-03-30)
+Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
-Platform: i686-pc-linux-gnu (32-bit)
+Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -25,6 +25,10 @@
Attaching package: 'gdata'
+The following object(s) are masked from 'package:stats':
+
+ nobs
+
The following object(s) are masked from 'package:utils':
object.size
@@ -131,7 +135,7 @@
List of 12
$ rowInd : int [1:32] 31 17 16 15 5 25 29 24 7 6 ...
$ colInd : int [1:11] 2 9 8 11 6 5 10 7 1 4 ...
- $ call : language heatmap.2(x = x, scale = "column", col = cm.colors(256), tracecol = "green", margins = c(5, 10), ColSideColors = cc, RowSideColors = rc, ...
+ $ call : language heatmap.2(x = x, scale = "column", col = cm.colors(256), tracecol = "green", margins = c(5, 10), ColSideColors = cc, RowSideColors = rc, density.info = "density", ...
$ colMeans : Named num [1:11] 6.188 0.406 0.438 2.812 3.217 ...
..- attr(*, "names")= chr [1:11] "cyl" "am" "vs" "carb" ...
$ colSDs : Named num [1:11] 1.786 0.499 0.504 1.615 0.978 ...
@@ -147,7 +151,7 @@
.. | |--[dendrogram w/ 2 branches and 3 members at h = 40.8, midpoint = 0.75, value = 198]
.. | | |--leaf "Chrysler Imperial" ( value.Chrysler Imperial = 66 )
.. | | `--[dendrogram w/ 2 branches and 2 members at h = 15.6, midpoint = 0.5, value = 132]
- .. | | |--leaf "Lincoln Continental" ( value.Lincoln Continental = 66 )
+ .. | | |--leaf "Lincoln Continental" ( value.Lincoln Continental = 66.1 )
.. | | `--leaf "Cadillac Fleetwood" ( value.Cadillac Fleetwood = 66.2 )
.. | `--[dendrogram w/ 2 branches and 5 members at h = 102, midpoint = 1.62, value = 290]
.. | |--[dendrogram w/ 2 branches and 2 members at h = 40, midpoint = 0.5, value = 111]
@@ -161,26 +165,26 @@
.. `--[dendrogram w/ 2 branches and 23 members at h = 262, midpoint = 6.33, value = 716]
.. |--[dendrogram w/ 2 branches and 7 members at h = 103, midpoint = 2.06, value = 306]
.. | |--[dendrogram w/ 2 branches and 2 members at h = 33.6, midpoint = 0.5, value = 73.8]
- .. | | |--leaf "Valiant" ( value.Valiant = 35.0 )
+ .. | | |--leaf "Valiant" ( value.Valiant = 35 )
.. | | `--leaf "Hornet 4 Drive" ( value.Hornet 4 Drive = 38.7 )
.. | `--[dendrogram w/ 2 branches and 5 members at h = 51.8, midpoint = 1.62, value = 233]
- .. | |--[dendrogram w/ 2 branches and 2 members at h = 14.0, midpoint = 0.5, value = 93.2]
+ .. | |--[dendrogram w/ 2 branches and 2 members at h = 14, midpoint = 0.5, value = 93.2]
.. | | |--leaf "AMC Javelin" ( value.AMC Javelin = 46 )
.. | | `--leaf "Dodge Challenger" ( value.Dodge Challenger = 47.2 )
.. | `--[dendrogram w/ 2 branches and 3 members at h = 2.14, midpoint = 0.75, value = 139]
.. | |--leaf "Merc 450SLC" ( value.Merc 450SLC = 46.4 )
- .. | `--[dendrogram w/ 2 branches and 2 members at h = 0.983, midpoint = 0.5, value = 93]
+ .. | `--[dendrogram w/ 2 branches and 2 members at h = 0.983, midpoint = 0.5, value = 92.9]
.. | |--leaf "Merc 450SE" ( value.Merc 450SE = 46.4 )
.. | `--leaf "Merc 450SL" ( value.Merc 450SL = 46.5 )
.. `--[dendrogram w/ 2 branches and 16 members at h = 142, midpoint = 3.59, value = 409]
- .. |--[dendrogram w/ 2 branches and 4 members at h = 14.8, midpoint = 0.875, value = 75]
+ .. |--[dendrogram w/ 2 branches and 4 members at h = 14.8, midpoint = 0.875, value = 74.9]
.. | |--leaf "Honda Civic" ( value.Honda Civic = 17.7 )
.. | `--[dendrogram w/ 2 branches and 3 members at h = 10.4, midpoint = 0.75, value = 57.2]
.. | |--leaf "Toyota Corolla" ( value.Toyota Corolla = 18.8 )
.. | `--[dendrogram w/ 2 branches and 2 members at h = 5.15, midpoint = 0.5, value = 38.4]
.. | |--leaf "Fiat X1-9" ( value.Fiat X1-9 = 18.9 )
.. | `--leaf "Fiat 128" ( value.Fiat 128 = 19.4 )
- .. `--[dendrogram w/ 2 branches and 12 members at h = 113, midpoint = 2.30, value = 334]
+ .. `--[dendrogram w/ 2 branches and 12 members at h = 113, midpoint = 2.3, value = 334]
.. |--leaf "Ferrari Dino" ( value.Ferrari Dino = 34.5 )
.. `--[dendrogram w/ 2 branches and 11 members at h = 74.4, midpoint = 3.61, value = 300]
.. |--[dendrogram w/ 2 branches and 5 members at h = 64.9, midpoint = 1.25, value = 148]
@@ -233,3 +237,6 @@
..$ color: Factor w/ 254 levels "#80FFFFFF","#81FFFFFF",..: 1 1 2 3 4 5 6 7 8 9 ...
>
>
+> proc.time()
+ user system elapsed
+ 1.427 0.067 1.487
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