Displaying 20 results from an estimated 4000 matches similar to: "heatmap row cell size"
2007 Feb 18
0
r-help@stat.math.ethz.ch
doh-trying again- this time remember text only.
Hello all- I am having trouble with the cell sizes that heatmap
defaults too. I have a matrix of 160 rows and 5 columns that I am
trying to display with heatmap(). When I do this, the cells default to
really wide and very short. This makes the labels for the rows very
hard to read, in fact the only way I can read them is to make the jpeg
output
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]),
2009 Sep 12
0
consistent results with heatmap.2
Hi,
I am trying to create a heatmap with some specific requirements. Specifically,
I need to be able to center the color-scale around 0, and I need to truncate the
data so that a few extreme values do not cause the rest of the heatmap to appear
black (on a red/green scale).
After reading through and experimenting with heatmap, heatmap.2, heatmap_plus,
and heatmap_2, I believe heatmap.2 will
2010 Sep 08
1
saving heatmaps in graphical format that can be edited in graphic editor tool
I generated a heatmap in R using the following commands:
> mydata <- read.csv(file="Data.csv", header=TRUE, sep=",")
> mydata <- mydata[rowSums(mydata[,-1]^2) >0, ]
> rownames(mydata)=mydata$Name
> mydata <- mydata[,2:253]
> mydatamatrix <- data.matrix(mydata)
> mydatascale <- t(scale(t(mydatamatrix)))
> hr <-
2010 Sep 08
2
saving heatmaps in graphical format that can be edited in graphic editor tools
I generated a heatmap in R using the following commands:
> mydata <- read.csv(file="Data.csv", header=TRUE, sep=",")
> mydata <- mydata[rowSums(mydata[,-1]^2) >0, ]
> rownames(mydata)=mydata$Name
> mydata <- mydata[,2:253]
> mydatamatrix <- data.matrix(mydata)
> mydatascale <- t(scale(t(mydatamatrix)))
> hr <-
2011 Apr 11
1
heatmap clustering dendrogram export
Hi,
I am a beginner for R.
I had use gplots to generate a heatmap as following:
>heatmap.2(matrix, col=topo.colors(75), dendrogram="column", Rowv=FALSE,
trace="none", key=TRUE, keysize=0.8, density.info="none", cexRow=0.2,
cexCol=0.6)
It work well. It generate heatmap whith rcolumn clustering dendrogram and I
can export a very nice graph. But I don not know how
2010 Sep 22
0
How to Ignore NaN values in Rows when using hclust function in making Heatmap??
I am making heatmaps for a dataset (~ 300*600 matrix) with the following R
script (I am not familiar with R and this is the first time I am using it).
library("gplots")
library("Cairo")
mydata <- read.csv(file="data.csv", header=TRUE, sep=",")
rownames(mydata)=mydata$Name
mydata <- mydata[,2:297]
mydatamatrix <- data.matrix(mydata)
mydatascale
2009 Apr 07
2
heatmap.2 no reordering of the columns and rows
Hi,
I need to generate a heatmap on a square matrix and wouldn't want to reorder the columns and the rows on the heatmap display.
I have used the options Rowv=NULL and Colv=NULL but doesn't seem to work. Following is a snippet of the heatmap function i am using.
args <- commandArgs();
inputfile <- args[2]
imgfile <- args[3]
bitmap(imgfile, height=15, width=15, res=100,
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 24
1
Saving heatmaps as PDFs
Hi,
I'm trying to save heatmaps as PDFs. However, the PDF version of the
heatmaps (Heatmap_CAFvsTNF_run2.pdf) is blurred when compared to its
counterpart, which was saved manually by using the software
"Grab" (Heatmap_CAFvsTNF_run2.tiff).
-----R code--------
sample_output <- "stroma_run2"
filename <-
2011 Apr 18
0
heatmap.2 - change column & row locations; angle / rotate
Hi Chakravarthy,
[dont forget to Cc the list for useRs with the same Q.]
If you're trying to reuduce the isze of your row or column labels, i
think the following arguments of heatmap.2 {gplots} is what you want to
adjust- 'cexCol' and 'cexRow'.
Specifically on my question that you ask about, i found the BioC forum
helpful:
2004 Nov 11
2
Row labels are skewed in 'heatmap' (PR#7358)
Full_Name: Peter Fischer Hallin
Version: Version 1.8.1
OS: Irix64
Submission from: (NULL) (130.225.67.236)
I've made a script look like this:
exp <- read.table("graph/1933672048.cluster.data")
exp <- as.matrix(exp)
postscript("graph/1933672048.cluster.data.ps")
heatmap(exp,scale="none",cexCol=0.4,cexRow=0.2,col=custom,margins=c(5,5))
The row labels
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.
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
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,
2004 Feb 16
1
labRow/labCol options in heatmap()
The function heatmap() allows to specify row/column labels
via the options labRow/labCol. From the code of heatmap(),
I understand that when no labels are specified, the row/column
labels (or indices) of the input matrix are taken as labels and
re-ordered together with the rows and columns of the matrix before
plotting, whereas labels supplied via labRow/labCol are plotted
in the original order.
2010 Jan 26
2
heatmap.2 color range
Hi,
I'm trying to create a heatmap with color ranges for different values in my
matrix. For example:
If x > 5 , use orange gradient
if x < 1.5, use red gradient
.....
Right now I have the following:
orgPal<-brewer.pal(3,"Oranges")
bluPal<-brewer.pal(3,"Blues")
redPal<-brewer.pal(3,"Reds")
grad <- ifelse(randMat >
2011 Jun 09
0
How to shift the heat map
Hi, what i need is as the example i attached in the box plot. As you can
see, the boxplot have margins and it kind
of follow the coding I've added, but, it does not happen for the heat
map. Could you help me with this.. Thanks in advance.
the following is the coding i've used:
# Draw the heatmap
# heatmap.r
#
# Purpose: Create a heatmap
#
# Input: Data matrix as
2012 Feb 27
1
row names of a heatmap on left hand side
Hello R Gurus,
I have a matrix for which I am doing a heatmap using heatmap.2. I want to
put the rownames on the lefthand side instead of the right side of the
heatmap. how can i put the rownames on left hand side: I have already tried
axis but could not make it work
ccc<-structure(c(1, 0.283300333755851, 0.237863231117007,
0.0148696794159253,
-0.0780756406815149, -0.106161465097659,
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>