similar to: Off Topic: UPS units and heat generation

Hello, I have a large data set from RNA sequencing and I am trying to make a heat map of my data. I have am having issues formatting my heat map figure. My data set is large with the log2 fold change for over 6oo genes across 4 treatments. My csv file is formatted as such: Gene Drought Ozone Temp1 Temp2 Glyma0041s00260

Hi, I have spatial data for plants that I would like to plot according to its radius using sysmbols(). Also I would like to color the circles according to an individual's age using heat.colors(17) [ages within the whole data set range from 0:16]. I have not found an easy way to assign ages (=a) a specific heat.color. Any suggestions? Thanks, Patrick x <- c(1,3,4,6,7,3,2,8,3,6,5,5) y

Hi all, I'm trying to using heat.color function in my data visualization. So, when I set col = heat.color(5), five different colors are displayed from red to weak yellow. But, now I want to know the color's keys or the names of the displayed heat.color. For instance, I think one of the five displayed colors seems to be 'red'. But, I'm not sure whether it is, also I don't

Dear All, I would like to do the following: make a plot of the world and color a few selected states. Some states have an associated scalar (i.e a simple number) and I would like to paint them using a heat map and show legend for the color map in the plot. One or two states do not have any number associated to them and are simply colored/filled according to a distinctive pattern that I choose. To

Hello, I am trying to make a heatmap in R and am having some trouble. I am very new to the world of R, but have been told that what I am trying to do should be possible. I want to make a heat map that looks like a gene expression heatmap (see http://en.wikipedia.org/wiki/Heat_map). I have 43 samples and 900 genes (yes I know this will be a huge map). I also have copy numbers associated with

If I want to create a heat map where I have a graphic of a US State with county borders, how do I import and work with the graphic image? The reason I would like to use R is so I can then define color parameters and quickly produce heat maps that correspond to various data in dataframes.   Thanks. Alison [[alternative HTML version deleted]]

Hi all! I want to generate a heat map from an all-vs-all comparison. I have the data, already scaled to 0-1. However, I have the values only for the comparisons in one way, and not for the comparisons between the same group (which are always 1), i.e. I have half the matrix and am missing the other half and the diagonal. What is a good way to get it into a form that ggplot2 can use for the

Hi all, I have read posts of heat map creation but I am one step prior -- Here is what I am trying to do and wonder if you have any tips? We are trying to map sequence reads from tumors to viral genomes. Example input file : 111 abc 111 sdf 111 xyz 1079 abc 1079 xyz 1079 xyz 5576 abc 5576 sdf 5576 sdf How may xyz's are there for 1079 and 111? How many abc's, etc?

Hello Everyone I am new to R I have drawn indifference curves using the program below (Contour Plot) u <- function(x, y) x^0.5 + y^0.5 x <- seq(0, 1000, by=1) y <- seq(0, 1000, by=1) a <- c(10, 20, 30) contour(x, y, outer(x, y, u),levels=a,col="blue") Now can any body please tell me how to draw Heat maps and that too on the same indifference curve plot (contour)

Dear List, Does there exist a function that produces a heat map like this one (image 3 of 4): http://www.tdameritrade.com/tradingtools/options360.html?a=HDY&referrer=http%3A%2F%2Fquery.nytimes.com%2Fsearch%2Fsitesearch%3Fquery%3Dheatmaptype%3Dnyt In addition to colors, two other main features I am intersted in are: 1. Proportionality in the size of the grid. 2. Mose-over capability. I may

I was wondering if someone could point in the direction of a package that could generate not heatmaps, but something like a unidimensional heat map. I might be mistaken, but it seems like image and heatmap are an overkill for such a simple task. For example, if I have a data frame: x<-data.frame(myname=paste("value",1:10,sep=""),a=1:10,b=sample(1:10,10,replace=T)) I'd

I'm experiencing a very unusual problem with a few of my sipuras. They keep over heating after minimal usage. I unplug them and let them sit for 15 minutes and it starts working fine. The other way around is that I put a fan on it or something to keep it cooling. Has anyone else experienced this or are they just defective units? Regards, Mohammed Salim EZZI Telecom, Inc.

Hi, I use heatmap.2 and heat.colors. Is it possible to specify the colors in that way that all values below, for instance, 1.5 should be coloured red, values between 1.5 and 1.7 green and above 1.7 black? Many thanks -- View this message in context: http://r.789695.n4.nabble.com/specify-heat-colors-tp2300139p2300139.html Sent from the R help mailing list archive at Nabble.com.

Hello all, I am trying to cluster similar rows of a data matrix together using hierarchical clustering and display the results in the form of a heat map. In a Heat map, is it possible to get the order in which the rows will be clustered , starting with the first rows joined into a group and then followed by other groups added. I thought i could extract the order by using $rowInd, but looks like

Hi, what i need is as the example i attached in the box plot. As you can see, the boxplot have margins and it kind of follow the coding I've added, but, it does not happen for the heat map. Could you help me with this.. Thanks in advance. the following is the coding i've used: # Draw the heatmap # heatmap.r # # Purpose: Create a heatmap # # Input: Data matrix as

I have a this new AMD X2 4800+ x86_64 box that works great and runs centos 4.3 x86_64 like a champ. I have 4 old machines running slackware, redhat 7.3 and redhat 9 and centos 4.3 i386. I would like to take the image of the disk (or something else equivalent) and run some kind of i386 emulation on the X2 box so I can run those old images when I need to and scrap the 4 old boxes. Heat and

Hey, I'm trying to generate a heat map of 30,000 fragments from probably 5-10 samples. Windows complains about memory shortage. Should I resort to Unix system? Also, if I only plot 1000 fragments out, they can finish it rather fast. 5000 would take more than 10 minutes. I don't know what to expect for 30,000... And on the side note, it seems like R only uses up to 50% of CPU while doing

Dear Experts, I am using the below script to generate the heat map of gene expression data. I am using Hierarchical Clustering (hclust) for clustering. Now I want to compare different clustering parameters such as *K-means* clustering, Model Based Clustering, I have two queries: 1. How to incorporate different clustering method in the same code? 2. Is this possible to implement pvclust in the

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

Hello, I am facing a problem in drawing heat map using R. I have a 70X3 matrix and I want to draw a heat map with 1 coloumn on X axis another on Y axis and want to show the value of 3rd coloumn using heat colours. Could you please help me with this . Thank you . Regards, Sumit [[alternative HTML version deleted]]