similar to: heatmap question

Dear R users, I have a question regarding how to make row labels readable in a heat map. I have successfully made a heat map using function "heatmap.2" in the package "gplots". However, as there are many rows in the heat map, I have difficulties labeling them (heatmap.2 provides a parameter "labRow" to label the row names, but as I have too many rows, I can not make

Hi all, new to this forum I'm try to using R to draw a heatmap of my RNA-seq data before doing that I did a log2 transformation of my data and produce a lot -inf in the matrix when I try to use the heatmap function, it seems can not deal with the -inf so I was wondering how to deal with these gene with 0rpkm(they are not 0 in all samples, so I want to keep them in the heatmap) thanks -- View

Hi, I would like to change the font type (to courier) of my rows labels when I plot a heatmap with R. I have used cexRow=0.7 to modify the size but didn't find anything regarding font type. heatmap(as.matrix(cebpa50), margins=c(5,10) , Colv=NA , scale="column", col=col4, cexRow=0.7) Thanks, Ben

I would like to draw horizontal or vertical lines on a heatmap to highlight the clusters at some specified cut depth of the dendrogram. As a hacked example, the following code would work if I could set the coordinates of the top and bottom of the false color image correctly (ymin and ymax), but the correct values seem to depend on the output device and its size. I realize that heatmaps use a 2x2

Dear all, I have a data set which is 100 \times 100 matrix. I made a heatmap of the data. The xlim and ylim are both shown to be c(0,1). I want to make both the xlim and ylim to be c(0,100). So the heatmap correspond to the 100 \times 100 locations. Thank you. Hannah [[alternative HTML version deleted]]

Hi all, I'm trying to use heat.map to display some data. The data is originally in csv format and when I read it in R using read.table I get: a b c d e 1 A 1 1 1 1 2 B 1 0 1 1 3 C 0 1 0 1 4 D 1 1 1 0 5 E 1 0 0 0 The problem is, that for heatmap I need a numerical matrix. When using data.matrix I get: a b c d e [1,] 1 1 1 1 1 [2,] 2 1 0 1 1 [3,] 3 0 1 0 1 [4,] 4 1 1 1 0 [5,] 5 1 0 0 0 So

Hi all, I have a matrix with values between 0 and 1. I want to plot this matrix on a heat map so anything >0.05 is blue, anything <=0.05 and >0.01 is yellow, and anything else is grey. I am using the heatmap.2 function. I searched around but did not find an efficient way to set colour ranges as I described. Could anybody give some hints? Thank you in advance. Wendy -- View this

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

Dear R Community, I am trying to create an heatmap for the following set of data: ##example of data matrix o4 V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14 V15 V16 V17 V18 green 27 28 29 29 28 28 26 25 25 23 23 22 22 21 21 22 22 22 yellow 6 8 8 7 7 7 6 6 6 7 7 7 6 6 6 6 6 5 red 15 15 15 15 15 15 14 13 12 11 12 10 9 8 7 6 8 9 pink

Hi folks, I am wondering if the following is possible: I want to control the arguments sent to a function by string variables. For example, instead of > heatmap.2( A, col=greenred(75) ) I would want to have something like: > heatmap.2 ( paste(A, "col=greenred(75)", sep=",") ) Is this possible to do that? Thanks, D.

Basically, I have the location data for about 1,000 pitches. I can get them to show up correctly on normal plots, but I am genuinely messed up on heatmaps. > location <- read.csv('C:/Users/William/Downloads/09Location.csv') > location <- as.matrix(location) Like I said, that can get a plot fine. Should I use image or heatmap? For the record, I want something like

Dear all, I made a large plot and wanted to save it as a tif file. I first opened and specified the size of the window. windows(12,17,rescale="fixed") Then I plot a heatmap using heatmap() when I saved the plot by using "Save as" in the file menu or savePlot("heatmap", type="tif"), the plot in the output tif file is truncated. Only the upper part of the

Hey, I am still working on my heat map (for those who are read my previous post about row.names)… Now, I would like to save my heat map.2 in .png or .tiff in order being able to work on the picture in photoshop, but it doesn't work. I'am using (as I have found on some forum) > png("heatmap.2.png) # and it just doesn't work. when I try doing it with::

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

Hello R-Users! I'm using a heatmap to visualize a matrix of values between -1 and 3. How can I set the colors so that white is zero, below zero is blue of increasing intensity towards -1 and above zero is red of increasing intensity towards red? I tried like this (using the marray and gplots packages from bioconductor): mcol <- maPalette(low="blue", mid="white",

I have a huge dataset(15k X 18) and tried to use the heatmap in R to examine the patterns. However, I found that heatmap and heatmap.2 gave me completely different outputs. Here are the codes: ------------ > dim(as.matrix(data.dcpm)) [1] 15462??? 18 > > heatmap(as.matrix(data.dcpm), col=topo.colors(100)) > heatmap.2(as.matrix(data.dcpm), col=topo.colors(100), key=TRUE,

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) <-

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.

Hi, I'm kinda new of the R world. I need to use the heatmap or heatmap.2 function to plot correlation values. 2 questions: - how can I specify a color palette? (would like to have a transition from blue(-1) to white(0) to red(1)) - how can I use heatmap.2 imposing a specific order (like hclust.order)? I mean, I don't want heatmap.2 to re-cluster/re-order my data but just to plot them

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!