Displaying 20 results from an estimated 2000 matches similar to: "Change font type for rows on Heatmap"
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
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.
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 <-
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 <-
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
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
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
2016 Apr 18
2
heatmap2 error key
Hi I am trying to understand what happen with the heatmap.2 code that it
used to work (last used in October 2015). I am able to get a heatmap but my
colour key doesn't come up and instead I get an error in all my files the
used to work. Does anyone has any idea of what could have changed? or how
to fix this.
Thanks.
#
Error in seq.default(min.raw, max.raw, by = min(diff(breaks)/100)) :
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,
2009 May 16
6
Modificando heatmaps
Hola a todos,
Estoy trabajando con la función heatmap.2() de la libreria ggplots. A
continuación encontrarán un ejemplo de la estructura de mis datos y el
código para generar el gráfico que me gustaría modificar:
# Datos
set.seed(123)
x <- matrix(rnorm(8*30), ncol = 8)
rownames(x) <- paste(''GM10A'',1:30,sep="")
colnames(x) <-
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]),
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.
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,
2008 Nov 17
1
HELP ON SCALING GENE EXPRESSION DATA TO -1,0,1
Hello R-Community,
I am a rookie in R and I am fascinated with the power of bio computing
by R. I am analysing gene expression data from Real time PCR. I have
used absolute gene quantitation to measure gene copy number in all my
transcripts. All my data has been normalised them to a housekeeping
gene, which is constitutive expressed.
My problem is as follows.
After normalising some of the genes
2012 Mar 20
0
labeling rows in heatmap.2
how can i put the row labels on the left hand of the heatmap in heatmap.2?
abnr<-structure(c(1, 0.678622097406395, 0.670294749652918,
-0.0016314464654279,
-0.000519068106572792, 0.199581999119988, -0.0106623494189115,
0.0840111691399559, -0.0461494399639137, 0.249279171677728, NA,
1, 0.757114062773504, 0.0352642759270137, -0.0255518450373996,
0.0943268190664674, -0.0536269679247722,
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
2011 Mar 28
2
How to save heatmap as image or pdf
Hello Everyone,
I am using R for creating heatmap from a square matrix. Below is my script
to do so
my_map <- read.csv("Desktop/input.csv", sep=",")
my_matrix <- data.matrix(my_map)
my_heatmap <- heatmap(my_matrix, Rowv=NA, Colv=NA, col = cm.colors(256),
scale="column", margins=c(5,10))
I get a beautiful plot as output, but I could not save this plot
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