similar to: Heat map on large sample size

Hi, Let say I have this matrix: > mat<-matrix(cbind(rnorm(20),rnorm(20)), ncol = 2) And I want to rescale values of column [,1] and [,2] using values from row 1 to 5, such that the values of row 1:5 should be rescale to the same amplitude (kinda like take the z-score of population from row 1:5). column 1 and 2 are two different samples need to be compared. I hope I made myself clear

Hi all, What parameter should I feed to the hist function to draw a line, not bar graph for a histogram? Smoothed line would be great too. I've looked at curve() for normal distribution but it's not what I need. I need some curve on top of the histogram (fit to the actual data). Just as a way to illustrate, rather than bargraph. Thanks -- Regards, Anh Tran UCLA NeuroOncology Lab

Hi all, I recently found out that R does not utilize fully the Duo Core capability when you only run one instance of R. I did some number crunching today and it seems that if I only open 1 R console, it uses 50% of my CPU (either 50-50 or 100-0 on 2 cores). Then, I open the second instance and divide the work into two parts, and run them parallelly, they seems to utilize 100% of my CPU. So, my

I'm trying to use combine c('a','b','c','a','c') into 'a, b, c', the order does not matter. paste(c('a','b','c','a','c'), collapse=', ') yields 'a, b, c, a, c'. Any idea? -- Regards, Anh Tran [[alternative HTML version deleted]]

Hi, Here's the data we have: > rs[1:5,] probe_id f1 f2 f3 f4 M A f 1 A_68_P20002076 2 58 0 0 1.51778114 6.344453 59 2 A_68_P20002775 22 8 15 0 0.43419304 5.488819 59 3 A_68_P20005791 43 3 0 0 0.05698666 9.830594 59 4 A_68_P20005805 11 34 0 0 1.71076835 6.624038 59 5 A_68_P20006729 16 44 0 0 0.85498261 6.044229 59 I want rs$f be the max of f1, f2, f3,

Hi, Is there away to print a short table out along side with a plot? I'm thinking about doing a par(mfrow = c(1,2)) Then, the plot is on one side, summary result on the other. Is there any quick way to print out a data.frame in table format? Thanks -- Regards, Anh Tran [[alternative HTML version deleted]]

Hi all, I'm putting a few plots together and wondering what format would be best to export a few scatter plots to Illustrator to make a figure. I'm thinking about overlaying some plot in Illustrator, so the export file type has to be transparent for Illustrator (version 10). I tried PNG and TIFF, but it does not seems to have transparency that is recognized by Illustrator (or Photoshop for

Hi all,I know this topic has came up multiple times, but I've never fully understand the apply() function. Anyway, I'm here asking for your help again to convert this loop to apply(). I have 2 data frames with the following information: a1 is the fragment that is need to be covered, a2 is the probes that cover the specific fragment. I need to count the number of probes cover every given

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

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

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]]

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

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

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 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

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?

Hi, What's one way to convert an integer to a string with preceding 0's? such that '13' becomes '00000000013' to be put into a string I've tried formatC, but they removes all the zeros and replace it with blanks Thanks -- Regards, Anh Tran [[alternative HTML version deleted]]

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