[Rd] row-side color bars do not reverse properly in heatmap (PR#7972)

[krc]

Full_Name: Kevin R. Coombes
Version: 2.1.0
OS: Windows XP
Submission from: (NULL) (143.111.224.169)


When revC = TRUE and RowSideColors is set to a list of colors in heatmap, then
the image and dendrogram are inverted, but the row-side color map does not
change. The following script illustrates the problem.

##
set.seed(1023)
# generate columns of two different types
d1 <- matrix(rnorm(100*6, rnorm(100, 0.5)), nrow=100, ncol=6, byrow=FALSE)
d2 <- matrix(rnorm(100*4, rnorm(100, 0.5)), nrow=100, ncol=4, byrow=FALSE)
# join them together
dd <- cbind(d1, d2)
# label them with different colors
cols <- rep(c('blue', 'green'), times=c(6,4))

# change the order of the columns and the matching labels
# to show that reordering occurs in one case in heatmap
col.order <- sample(10)
dd <- dd[, col.order]
cols <- cols[col.order]

# compute the dendrogram to be used in the display
hc <- hclust(dist(dd, 'euclid'))

# get the correlation matrix
m <- cor(dd)

# this version works correctly
heatmap(m, Rowv=as.dendrogram(hc), symm=TRUE, revC=FALSE,
RowSideColors=cols)
#this version reverses the dendrogram and image, but not the colors
heatmap(m, Rowv=as.dendrogram(hc), symm=TRUE, revC=TRUE,
RowSideColors=cols)

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[Rd] Sweave bug using 'FDR' in chunk label (PR#9567)

[krc]

Full_Name: Kevin Coombes
Version: 2.4.0
OS: Windows XP
Submission from: (NULL) (143.111.22.24)


I'm running R 2.4.0 on a Windows XP machine, with only the default packages
loaded.

Running Sweave or Stangle on the following Rnw file:
--
% bug.Rnw
\begin{document}
Demonstrate an Sweave/Stangle bug.
<>=
sessionInfo()
@ 

<>=
x <- 1
@ 
<>=
y <- 2
@ 
<>=
<>
<>
@ 

\end{document}
---

produces an error message:

> Stangle("bug.Rnw")
Writing to file bug.R 
Warning message:
reference to unknown chunk 'getFDR' in: Sweave(file = file, driver = driver,
...) 


Here is the relevant part of the "bug.R" file produced by Stangle.  Note that
the label has been truncated on chunk2 (should be getFDR) but is not affected on
chunk3. Also note that chunk4 has not been expanded properly.

###
### chunk number 2: getF
###
x <- 1

###
### chunk number 3: getFDX
###
y <- 2

###
### chunk number 4: problem
###
y <- 2

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[Rd] Sweave processes comments incorrectly (PR#9073)

[krc]

Full_Name: Kevin R. Coombes
Version: 2.1.0
OS: Windows XP
Submission from: (NULL) (143.111.22.24)


I have a source file "devel.Rnw" that uses the LaTeX foils class and ppower4 to
produce a PDF presentation file.  It starts with a commented note to myself as
follows:

 begin source example 
%
%  Remember to update the hypersetup to include individual lecture
%  titles, change the leftheader to include the lecture title, and
%  then start at \begin{document} 
%  Also, produce a printable (black and white version) according
%  to the cues immediately following \begin{document}.
%  Compile this document with:
%pdflatex .tex
%  and then:
%ppower4pb .pdf .pdf
%
\documentclass[Screen4to3,25pt,headrule,footrule]{foils}
\usepackage[pdftex]{color}  %for colors
\definecolor{Teal}{rgb}{0.0,0.47,0.46}
%% more colors and packages omitted from bug report
\begin{document}
\hypersetup{pdfpagetransition=Replace}

 end source example 

When processed using Sweave, the \begin{document} comments are expanded to
actual LaTeX commands, causing a later latex to fail.  That is, the output of
running Sweave() on this file begins:

 begin source example 
%
%  Remember to update the hypersetup to include individual lecture
%  titles, change the leftheader to include the lecture title, and
%  then start at \usepackage{c:/R/rw2010/share/texmf/Sweave}
\begin{document} 
%  Also, produce a printable (black and white version) according
%  to the cues immediately following
\usepackage{c:/R/rw2010/share/texmf/Sweave}
\begin{document}.
%  Compile this document with:
%pdflatex .tex
%  and then:
%ppower4pb .pdf .pdf
\documentclass[Screen4to3,25pt,headrule,footrule]{foils}
\usepackage[pdftex]{color}  %for colors

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