Displaying 20 results from an estimated 500 matches similar to: "Unexpected behaviour for RowSideColors in function heatmap"
2009 Jul 21
1
problem with heatmap.2 in package gplots generating non-finite breaks
I have written a wrapper for heatmap.2 called
heatmap.w.row.and.col.clust which auto-generates breaks using
breaks<-round((c(seq(from=(-20 * stddev), to=(20 * stddev))))/20,
digits = 2) #(stddev in this case = 2.5)
This has always worked well in the past but now I am getting an error
that non-finite breaks are being generated. Drilling down, it seems
that my wrapper is generating finite
2005 Jun 29
1
(PR#7972) row-side color bars ... in heatmap
Hi Kevin,
>>>>> "krc" == krc <krc at odin.mdacc.tmc.edu>
>>>>> on Mon, 27 Jun 2005 21:55:37 +0200 (CEST) writes:
krc> Full_Name: Kevin R. Coombes
krc> Version: 2.1.0
krc> OS: Windows XP
krc> Submission from: (NULL) (143.111.224.169)
krc> When revC = TRUE and RowSideColors is set to a list of
krc>
2010 Feb 23
2
heatmap.3
Hello again,
lately I have been playing a lot with heatmap functions,
in particular I complemented heatmap.2 with a nice feature from
heatmap.plus,
i.e. the possibility of assigning a matrix to ColSideColors so to take into
account more annotations.
Below is the code I introduced in heatmap.2, everything else is maintained
equal to heatmap.2:
if (!missing(ColSideColors)) {
#if
2007 Sep 05
1
problem formatting and positioning title in heatmap
I am using heatmap with the arguments below. The title size stays the
same no matter what I set cex.main to. Is this expected? Can I adjust
the title size in heatmap?
Also, the position of the main title is at the very upper edge of the
output and if I use a "\n" to stack the title the upper line is out of
bounds and doesn't show up.
I am outputting to pdf.
Any help? Thanks,
2006 Apr 07
2
Dealing with missing values in HeatMap generation
Hi,
I want to generate a heatmap for my data (in a matrix). However, the
data has some missing values (represented as blank).
I get the following errors (with the blanks and with blanks replaced by
NA and including the option rm.na = TURE):
> filename = "input_heatmap.txt"
> g <- as.matrix(filedata)
> fg <- rainbow(nrow(g), start=0, end=.3)
> gg <-
2006 Jan 23
1
lines() in heatmap()
Hello!
I looked for help through google and the help-files and spend several
hours with trial and
error, but didn't find a correct way.
It's all about lines in a heatmap to separate different data block from
each other to underline
the significance of the found clusters!
The heatmap is build like that:
heatmap(X, Rowv=NA, Colv=NA, symm=TRUE, cexRow=0.3, cexCol=0.3)
I switched the
2009 Aug 19
1
moving color key in heatmap
Dear list,
I have a question on moving color keys when side color bars are added to a heatmap.
The R code below produces the color key in the upper left corner. Notice I have added side bars to the heatmap, but how could I move the color key below the image?
------
library(gplots)
data(mtcars)
x <- as.matrix(mtcars)
rc <- rainbow(nrow(x), start=0, end=.3)
cc <- rainbow(ncol(x),
2010 Mar 03
1
Heatmap reordering of dendrogram to hierarchical clustering
Dear list members,
I have been using R to create a heatmap where my data has continous
variables from 0 to 100.
When I create the heatmap, although the branches are correct, they do not
order themselves so that the row with the most zeros is at one end and the
row with the most 100s is at the other, which is what I would like them to
do, so as to create a colour gradient down the graphic.
I have
2004 Dec 15
1
hclust and heatmap - slightly different dendrograms?
Good afternoon,
I ran heatmap and hclust on the same matrix x (strictly, I ran
heatmap(x), and hclust(dist(t(x))), and realized that the two
dendrograms were slightly different, in that the left-right
arrangement of one pair of subclusters (columns) was reversed in the
two functions (but all individual columns were grouped correctly).
Looking through the code for heatmap as a most definite
2005 Jun 27
0
row-side color bars do not reverse properly in heatmap (PR#7972)
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 <-
2004 Sep 07
3
heatmap help
Dear R wizards,
Hopeful someone can help me with what I believe is a pretty simple task. I
pretty new to R so some (much) of the obvious escapes me. How do I get a
distance matrix into heatmap? What do I tell distfun if what I'm trying to
map is already an ordered distance matrix? I tried >heatmap(x,
distfun=as.dist(x)) where x is the distance matrix but R gave me an error.
Thanks in
2014 Sep 04
1
gplot heatmaps: clustering according to rowsidecolors + key.xtickfun
Hi there,
I have two questions about heatmap.2 in gplot.
My input is a simple square matrix with numeric values between 75 and
100 (it is a similarity matrix based on bacterial DNA sequences).
1. I can sort my input matrix into categories with rowsidecolors (in
this case, very conveniently by bacterial taxa). I do a clustering and
reordering of my matrix by Rowv=TRUE (and
2007 Oct 08
2
heatmap
Hi,
I am having troubles with heatmap(). I have a matrix containing pairwise
distance values and I want to plot this matrix with heatmap. I wonder
now what distfun is for. Is a distance matrix computed from my initial
matrix again and then plotted?
cheers,
andreas
2007 Jan 19
1
Error in heatmap()
Hi,
I run into following error when using heatmap() for data matrix "xx".
Any help is appreciated? "xx" contains many "NA"s.
> hv <- heatmap(data.matrix(xx))
Error in hclustfun(distfun(if (symm) x else t(x))) :
NA/NaN/Inf in foreign function call (arg 11)
Thanks a lot.
Yuhong
2012 Oct 01
2
Reading labels for very large heatmaps
Hello,
I have a large (919 X 919), hierarchically clustered heatmap that I would
like to read the labels off of. I have tried saving the figure in pdf
format and enlarging it until I can see the labels, but if I make the labels
small enough to read (so that they don't overlap) using cexRow and cexCol,
they do not appear in the pdf. The limit seems to be anything below cexRow
or Col = 0.06.
2008 Jun 16
1
heatmap.2 dendogram algorithm
Hello
does anyone know what algorithm is used to produce the hierarchical
clustering in the gplots package using the function heatmap.2? I think it
may be the complete linkage clustering algorithm, but I can't find a source
that seems reliable.
Thank you and sorry if I posted this in the wrong place. If I have, please
let me know and I will move it to the appropriate list.
--
View this
2004 May 10
3
Colouring hclust() trees
I have a data set with 6 variables and 251 cases.
The people who supplied me with this data set believe that it falls
naturally into three groups, and have given me a rule for determining
group number from these 6 variables.
If I do
scaled.stuff <- scale(stuff, TRUE, c(...the design ranges...))
stuff.dist <- dist(scaled.stuff)
stuff.hc <- hclust(stuff.dist)
2001 Nov 06
4
ext3 on md0
Hi!
Is it safe to use ext3 on a md0 device on 2.2.19?? 2.4.x??
/Pär-Ola Nilsson
2011 Mar 02
2
clustering problem
Hi,
I have a gene expression experiment with 20 samples and 25000 genes each.
I'd like to perform clustering on these. It turned out to become much faster
when I transform the underlying matrix with t(matrix). Unfortunately then
I'm not anymore able to use cutree to access individual clusters. In general
I do something like this:
hc <- hclust(dist(USArrests), "ave")
2011 Oct 18
0
heatmap
Dear R users, need help with my heatmap. I will really approciate some help.
Given the matrix:
> head(x)
A B C D time
[1,] 0 8 0 0 1
[2,] 0 160 0 0 2
[3,] 0 175 0 0 3
[4,] 0 253 0 0 4
[5,] 79 212 0 0 5
[6,] 6 105 0 0 6
and call:
##------------ Heatmap --------------
library(RColorBrewer)
rc <- grey((nrow(x):1)/nrow(x))
heatmap(data.matrix(x[,1:4]),