similar to: heatmaps and layouts

Hi, I was trying to use par(mfrow) to put 4 heatmaps on a single page. However, I get one plot per page and not one page with 4 plots. What should I modify? Test code is given below: test = matrix(rnorm(60), 20, 3) pdf(file='test.pdf',width=10,height=8) par(mfrow=c(2,2)) heatmap(test) heatmap(test) heatmap(test) heatmap(test) dev.off() thanks! [[alternative HTML version deleted]]

The answer is "don't do that" because that function abuses par. Use lattice or ggplot2 with grid graphics to plot multiple heatmaps. https://stackoverflow.com/questions/15114347/to-display-two-heatmaps-in-same-pdf-side-by-side-in-r -- Sent from my phone. Please excuse my brevity. On July 23, 2017 5:11:32 AM PDT, Brian Smith <bsmith030465 at gmail.com> wrote: >Hi, >

Dear all, I've been trying to find how to compare tow different heatmaps but I'm having trouble getting the colors bar to be the same. I'm doing something like the following: library(gplots) dat<-cor(matrix(rnorm(100, m=10), nrow=10)) mat<-cor(matrix(rnorm(100), nrow=10)) dev.new() heatmap.2(mat, Rowv=NA, Colv=NA, col=redgreen(75), symm=TRUE, trace="none",

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.

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 <-

Hi, I have some data which I was plotting using image(). I wanted to add a vertical color key to the plot and I found that heatmap.2 in gplots does let me add a color key. However, I was thinking of a vertical bar with the color range rather than the style that gplots provides. Is there any package (or code snippet) that would let me add a vertical color key to an image() or heatmap

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

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) <-

Hello all , I am beginner and new to this -R world. I have heard much about R and started working on it. I have some data of 20 business applications( y -axis) and Months( x-axis) and values as their score for every month . I tried to generate a heatmap with this data and got some good results. Can some one help me on how to generate the legend next to heatmap please... can some one send me

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 <-

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 <-

Using the heatmap function in mva, it seems to be hard to use different colors in the edges leading to different groups of objects, as commonly done in many heatmaps in the microarray graphics. Any suggestions? Thanks. max

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

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

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) >

I would like to use gridBase to place four separate heatmaps (actually, a stripped-down heatmap.2 from ght gregmisc package that contains only the "image" part) into four different viewports. I can get the placement correct, but I keep 'losing' the previous plot. Any suggestions? Here is some quick example code trying to put a heatmap into the left viewport and then

Hi all, I've got a set of gene expression data, and I'm plotting several heatmaps for subsets of the whole set. I'd like the heatmaps to have the same color distribution, so that comparisons may be made (roughly) across heatmaps; this would require that the color distribution and distance functions be based on the entire dataset, rather than on individual subsets. Does

(I have searched the email archives for discussions on this topic but have found nothing.) The help page for heatmap says: By default (scale = "row") the rows are scaled to have mean zero and standard deviation one. There is some empirical evidence from genomic plotting that this is useful. I offer two comments on that. 1. Since the heatmap function is general-purpose (that is, not in

Dear R-helper: Suppose we have a matrix: Gene sample1 sample2 Gcnt1 12.0000 52.80000 Max 8.8000 39.10000 Tmem176b 67.9000 304.70000 Shmt2 8.6000 42.40000 Rtn4 11.5000 57.70000 Il17re 7.6000 38.80000 Bclp2 6.2000 32.10000 Mobkl3 4.4000 32.20000 Akr1b10 3.4000 30.10000

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