Displaying 20 results from an estimated 5000 matches similar to: "large data set (matrix) using image()"
2004 Jan 04
5
Analyzing dendograms??
I have used heatmap to visualize my microarray data. I have a matrix of
M-values. I do the following.
#The distance between the columns.
sampdist <- dist(t(matrix[,]), method="euclidean")
sclus <- hclust(sampdist, method="average")
#The distance between the rows.
genedist <- dist(matrix[,], method="euclidean")
gclus <- hclust(genedist,
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,
2012 Feb 28
1
Unexpected behaviour for RowSideColors in function heatmap
Hello,
I have come across some unexpected behaviour of the function heatmap in the stats package. This looks like a bug to me, but I might have misunderstood something.
When calling the function in symmetric mode, the ColSideColors are plotted correctly, but RowSideColors appear in reverse order. This code (modified from the example on the help page) demonstrates the problem:
cU <-
2004 Dec 04
1
Wishlist: heatmap/image legend (PR#7402)
Full_Name: Elizabeth Purdom
Version: 1.9.1
OS: Windows XP
Submission from: (NULL) (171.64.102.199)
It would be great if heatmap and/or image had the option of printing a legend
bar on it somewhere that would indicate the ranges given by the colors in the
heatmap (i.e. a very small image rectangle with the same colors as in the
heatmap). Because heatmap is using layout, it seems pretty
2013 Dec 07
1
How to perform clustering without removing rows where NA is present in R
I have a data which contain some NA value in their elements.
What I want to do is to **perform clustering without removing rows**
where the NA is present.
I understand that `gower` distance measure in `daisy` allow such situation.
But why my code below doesn't work?
__BEGIN__
# plot heat map with dendogram together.
library("gplots")
library("cluster")
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 <-
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
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
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),
2004 Jan 07
1
Analyzing dendrograms
Ladies and Gentlemen,
As Johan Lindberg points out, the documentation for handling dendrograms
is sparse....Does anyone know who is responsible for or working on
development of tree methods and objects? I've written a couple of scripts
for my own use to translate between parenthetical (A(B(CD))) or binary
A00 B10 C11 D11 tree formats and cluster objects in R, but as an
inexperienced
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 <-
2007 Nov 22
2
Heatmap problem
Hi friends,
I used heatmap(as.matrix(y2),col=rainbow(256),scale = "column") to
generate the heatmap. But it did not show the code that which
color correspond the value. Is there any parameter for this in
heatmap()?
Thanks a lot!
Allen
[[alternative HTML version deleted]]
2007 Apr 25
1
heatmap and phylogram / dendogram ploting problem, ape package
I am having trouble displaying a dendrogram of evolutionary
relationships (a phylogram imported from the ape package) as the
vertical component of a heatmap, but keeping the hierarchical
clustering of the horizontal component. The relationships of the
vertical component in the generated heatmap are not that of the
dendrogram, although the ordering is.
In more detail, I am attempting to generate
2009 Sep 21
1
Specific criteria for color palette using heatmap.2
I'm trying to display the probability space of a function and wanted to see
specifically where the maximum posterior probability is.
data=read.table("PosteriorData",header=F)
mat=as.matrix(data)
heatmap.2(mat/max(mat,na.rm=T),dendrogram=c("none"),trace=c("none"),
Rowv=F,Colv=F,labRow=3*c(10:-10),labCol=3*c(-10:10),symm=T,col=rainbow(100))
As the
2005 Mar 24
2
font sizes for row.names of dendograms
Dear R
I recently performed a cluster analysis. It produced the dendogram no
problem but unfortunately the font size of the row.names were all cluttered
due to their large size
So I tried to change the font size using
plclust(cluster.results, labels=iris$specie, cex=0.8)
and R came back to me saying
Error in plclust(cluster.results, labels = iris$specie, cex = 0.8) :
unused argument(s)
2007 Jun 25
2
Re : Half of a heatmap
> I am trying to produce a heatmap of pairwise correlations, but since the matrix is
> symmetric, I only need either the upper or the lower triangle. I have scoured the
> web and R documentation, but I have not been able to find a way to produce such a
> figure. Is there a simple way to produce a heat map with only the part above or
> below the diagonal?
You might want to check
2008 Aug 06
2
Attempting to make a custom color spectrum to use in heatmap.2
Hello there! I'd just like to say in advance, "Thank you," for any help
and/or advice.
My problem is as follows:
I have a dataset that is made up of percentages. I've assigned my
"error" percentages a value of '-100', my "non-existent" percentages a
value of '0', and all my other percentages are normal values that range
from the high
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.
2012 Dec 04
1
How do I get internal nodes of dendograms produced by R?
I am using R for hierarchical clustering of a number of documents.
I have a distance matrix on which I have applied hclust method. When I plot
the result of hclust method, I can see the dendogram plotted. What I need
now is the dendogram stored as a tree in a data structure. My goal is to
automatically label all internal nodes. For that, I need to know, which
leaf nodes make a first level