similar to: Reg : Hello all.. help needed regarding heatmaps

I'd like to create a polar plot similar to those created by the polarFreq function in the openair package. However, this package seems to be specific to wind speed and direction, and requires a "ws" (wind speed) and a "wd" (wind direction) column. My data is unrelated to wind speed, but I'd like to be able to get a plot that does what polarFreq's plots do; I'd

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! I am trying to analyse my data using amova (http://www.oga-lab.net/RGM2/func.php?rd_id=pegas:amova): My input to R is a DNA sequence file, format=fasta dna<- read.dna("XX.fasta", format="fasta") #left other options as default d<- dist.dna(dna, model="raw") g<- read.table("XXX.design") Load necessary libraries: library(pegas)

Hello everbody, I am new to this mailing list and hope to find some help. I'm trying to get into the spatstat package and encountered two problems. First a graphical one: There is an example dataset called "finpines" which has several marks (http://www.oga-lab.net/RGM2/func.php?rd_id=spatstat:finpines) When I pass the given code from the website to R data(finpines)

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

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",

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 <-

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 <-

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.

I'm using R to create a heatmap from a matrix using heatmap.2 - and i want to group these images into one big image - What i usually use to achieve this is layout() - but this doesn't work, as heatmap.2 uses layout, and apparently layout does not work recursively. Does anyone have any suggestions on how to group together 2 images without layout, or how to make layout support recursive

How to adapt this piece of code but for: - gamma distribution - 3 parameter log normal More specifically, where can I find the specification of the parameter (lmom) for pelgam() and pelln3()? Lmom package info just gives: pelgam(lmom), lelln3(lmom), where lmom is a numeric vector containing the L-moments of the distribution or of a data sample. # Draw an L-moment ratio diagram and add a line for

Dear All, I'm having trouble tweaking a forest plot made using the R meta-analysis package metafor. I did the analysis based upon the correlation coeff from studies and plotted the corresponding forest plot easily > q2<-rma(yi,vi,mods=cbind(grupo),data=qim) > q2 > forest (q2,transf=transf.ztor,digits=3, ... ,alim=c(0,1),refline=.5) > text(-1.55,42,"Esp?cie

Greetings of Peace! I am new in R software. I want to use the correlation dimension corrDim in computing a map. I have installed the packages(fractal) in R. Now my problem is this, when I tried your example in the following site http://rgm2.lab.nig.ac.jp/RGM2/func.php?rd_id=fractal:corrDim  > library(fractal) > png(filename="corrDim_%03d_med.png", width=480, height=480) >

Dear List, Following the link below ( http://rgm2.lab.nig.ac.jp/RGM2/func.php?rd_id=plotrix:clock24.plot) I got an interesting polar plots which displayed my data and the time of observation. Thank you very much for providing such details. However, I have two set of data which I wish to display in the same polar plot. I tried using points to add the second data but could not succeed. That is,

hi, there: i have 2 questions associated with heatmap in heatmap.2{gplot}, there is a bar called "raw z-score" showing the coloring legend for each pixel. Where can I find that z-score's formulae? question 2, for example, I have 5 groups and I want to label each group with a color name from "#FF0000" to "#0000FF" evenly. so basically i need a vector like this:

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

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) >

Hi, I have been trying to add labels to the rows of a heatmap produced using image() function. It is simply not working. Here is what I did. A2Rplot.hclust(hcc,k=length(num),col.up="black",col.down=num,lty.up=2,lty.down=1,lwd.up=1,lwd.down=2,show.labels=FALSE) #used the above external program to create a colored dendrogram xsort <- x[1:nrow(x), hcc$labels[hcc$order]]

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]]