Displaying 20 results from an estimated 3000 matches similar to: "how to save a heatmap.2 in png /jpeg /tiff"
2008 May 14
4
Heatmap.2 - eliminate cluster and dendrogram
Using the heatmap.2 function, I am trying to generate a heatmap of a
2 column x 500 row matrix of numeric values. I would like the 1st
column of the matrix sorted from the highest to the lowest values -
so that the colors reflected in the first column of the heatmap (top
to bottom) go from red to green.
After sorting the matrix (z), I tried the following command, but the
data remains
2004 Sep 02
3
Problems with heatmap.2
Hi
When I give the command:
>
heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="row
",trace="none",col=greenred.colors(79))
The resulting heatmap has re-ordered my columns! This is time-course
data, and I don't want my columns re-ordered! Note from the help:
Rowv: determines if and how the _row_ dendrogram should be
reordered.
2009 Jan 20
1
heatmap.2 color issue
Dear All:
I tried to use heatmap.2 to generate hierarchical clustering using the following command:
heatmap.2(datamatrix, scale="row", trace="none", col=greenred(256), labRow=genelist[,1], margins=c(10,10), Rowv=TRUE, Colv=TRUE)
datamatrix is subset of a RMA normalized data subset by a genelist.
The problem is a lot of times, the z-score in key are from, like -5 to 15 or
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 <-
2010 Sep 18
1
Drawing Heatmap using gplots
Hi,
I am using heatmap.2 of gplots to make heatmaps of my the attached file. I
am giving my code for the same ..
library(gplots)
x=read.table("1.txt", header=TRUE)
mat=data.matrix(x)
heatmap.2(mat, col=greenred(75),
Rowv=TRUE,
Colv=TRUE,
distfun = dist,
hclustfun = hclust,
dendrogram = c("both"),
scale = c("row"),
na.rm=TRUE,
trace="none",
2006 Mar 06
2
Problems with heatmap.2 in the gregmisc package
Hi
Sorry to revisit an old problem, I seemed to solve this in 2004, only
for it to resurface :-S
I am trying to plot a heatmap, and I don't want the columns of my matrix
re-ordered. The function doesn't seem to behave as the help would have
you believe:
a <- matrix(rnorm(100),nr=20)
a.d <- dist(a)
a.hc <- hclust(a.d)
a.de <- as.dendrogram(a.hc)
# columns are re-ordered
2011 Jan 05
1
Heat map in R
Hello,
I am trying to make a heatmap in R and am having some trouble. I am very new
to the world of R, but have been told that what I am trying to do should be
possible. I want to make a heat map that looks like a gene expression
heatmap (see http://en.wikipedia.org/wiki/Heat_map).
I have 43 samples and 900 genes (yes I know this will be a huge map). I also
have copy numbers associated with
2010 Oct 08
2
Heatmap/Color Selection(Key)
Hi
I made heatmap of QTL based on Lod score. Where I have traits in columns and
marker data (rows). I can not cluster both column and rows as I need the
right order for marker data.
Can someone suggest me better way of generating heatmaps especially the
colour key I want to select to visualize the results which are more
interesting to look at.
> library(gplots)
>
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 Feb 11
2
heatmap.2 in gplots (PR#8587)
Full_Name: Shane Neph
Version: 2.2.1
OS: mac os x
Submission from: (NULL) (71.113.43.247)
While I found the names of the package authors and maintainer, I was
unsuccessful in finding any contact information.
The preliminary documentation for heatmap.2 is inconsistent in at least a couple
of places when discussing the suppression of one or more dendrograms (and
column/row ordering in general).
2012 Sep 07
3
Problem with duplicates in row.names
Hello,
I am drawing a heatmap with hundreds of genes. Everything work fine, except when I want to had the name of the genes as the row.names with
>row.names (a)<-a$Name
And there''s this things that duplicate are not allowed...
How can I do to allow duplicates ??? I don''t have the choice I can''t just have numbers .
Thanks for your help, I am new in R ...
Fred
2007 Aug 23
1
figure-definition and heatmap question
Hello,
I have two questions. I'd like to visualize data with a heatmap and I have the
following testcase:
x <- rnorm(256)
nx <- x + abs(min(x))
nnx <- 255/max(nx) * nx
x <- matrix(nnx, 16, 16)
rownames(x) <-
2005 Jul 27
3
Asymmetric colors for heatmap
> Dear expeRts,
>
> Currently, my colors are as follows:
> mycol <-
> c("blue1","blue2","blue3","blue4","black","yellow4","yellow3","yellow2","y
> ellow1")
> heatmap(snp, Rowv=NA, Colv=NA, col=mycol)
>
> However, I would like to have the following colors:
> bright blue ->
2005 Aug 22
2
problem building dendrograms to use with heatmap()
Hi,
I'm trying to build dendrograms to pass to heatmap().
The dendrograms I build plot properly, but when I pass them to heatmap() I get
the error message "row dendrogram ordering gave index of wrong length" (see
output log below).
I looked in the code of heatmap() and saw that the error was due to a NULL
return value from order.dendrogram(), which in turn got a NULL return value
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
2004 Jul 21
2
Cutting heatmap dendrogram
Hello,
I've been clustering my data using hclust and cutting the resulting tree
with cutree. Separately, I visualize the clusterings with heatmap. Is it
possible to have the dendrogram on the heatmap reflect the cutree results?
That is, instead of having one large dendrogram, it would have 4 or 25 in
the example below. Any guidance on if that's possible or not, and what
kinds of
2010 Feb 07
3
specifying colors in a heatmap/image -like plot
Hi,
I have searched for a solution but I failed to find an answer. I am hoping
you may be able to help me.
I have a data set where I have observations for a number of units (n =~40)
over a period of time (t =~100) and I have a variable (Z) that codes a
categorical variable for each observation. I want to produce a 2D plot where
time is on the x-axis and units are on the y-axis. Then each block
2011 Feb 09
2
heatmap-how to change the order of the rows (genes)
Hi,
I have a question about the heatmap dendrogram in R. I loaded my data
matrix in command heatmap(), and it gave me a heatmap accordingly, and the
rows (genes) also were clustered accordingly. But now I don't want the
genes clustered in that way, I have a new order of these genes, and want the
rows of the heatmap are drawed as the order I give. Could anybody help me
on that? Thank you!
2011 Oct 24
1
heatmap for plotting categorical matrix
Hi there,
I have a matrix like this:
> a4[1:20, 1:5]
194 211 294 314 315
GO:0000003 1 1 1 1 1
GO:0000072 0 0 0 0 0
GO:0000076 1 0 0 0 0
GO:0000082 1 3 1 1 1
GO:0000083 1 0 0 0 1
GO:0000086 0 1 0 1 1
GO:0000114 0 0 0 0 0
GO:0000115 0 0 0 0 0
GO:0000117 0 0 0 0 0
GO:0000160 0 0 1 0 0
2011 Aug 08
1
heatmap is producing unwanted horizontal and vertical lines?
Hello,
I must start by saying that I am an R novice and am sorry if this is a no-brainer...
I have an csv file that contains a grid of 300x300 data points. Each point represents
a 1Km square on a map. Each point is either a floating point number or NA. I load the
data in with:
data <- read.csv("matrix.csv", sep=',')
Convert the data to a matrix with:
data_matrix <-