similar to: World Heat/Rainbow Map

Dear All, I need to do something relatively simple: generate a map of Europe and paint the various states with different colors (only 3-4 are needed) according to a rule. I would like to keep it as simple as possible and the script resorting to the sp package that I found at http://bit.ly/Oc71ub is exactly what I am looking for (I need to repeat the exercise with Europe instead of

Dear All, I am pretty satisfied with R for my plotting, but there are a few subtleties which I cannot figure out. Consider figure 1 in the paper at the link below http://cxnets.googlepages.com/univ_citations.pdf Can I have the same kind of ticks in an R-generated figure (that is to say: ticks along the 4 axis, and in a log-log plot I'd like a larger tick for any power of 10). I did a bit

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

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

Dear All, I like very much figure 2.a) and 2.b) of this paper http://www.nature.com/srep/2013/130410/srep01640/pdf/srep01640.pdf and I probably need a similar visualization. Is anything like that doable in R? I have some experience with R and gadm (gadm.org), but that is only to produce maps colored according to a scalar. I do not know how to visualize maps with a "perspective", let

Hi Ralf, I tried the following > install.packages("RCurl") which went OK, but then same story when I tried to install tseries. > sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0 LAPACK:

Dear All, I am far from being a guru about parallel programming. Most of the time, I rely or randomForest for data mining large datasets. I would like to give a try also to the gradient boosted methods in GBM, but I have a need for parallelization. I normally rely on gbm.fit for speed reasons, and I usually call it this way gbm_model <- gbm.fit(trainRF,prices_train, offset = NULL, misc =

Dear All, Probably a one liner, but I am banging my head against the floor. Consider the following DF <- data.frame( x=1:10, y=10:1, z=rep(5,10), a=11:20 ) mn<-names(DF) but then I cannot retrieve a column by doing e.g, DF$mn[2] I tried to play with the quotes and so on, but so far with no avail. Any suggestion is welcome. Cheers Lorenzo

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

Dear All, I would like to be able to plot histograms/densities on a semi-log or log-log scale. I found several suggestions online http://tolstoy.newcastle.edu.au/R/help/05/09/12044.html https://stat.ethz.ch/pipermail/r-help/2002-June/022295.html http://www.harding.edu/fmccown/R/#histograms Now, consider the code snippet taken from http://www.harding.edu/fmccown/R/#histograms # Get a random

Dear All, I am struggling with the following problem: I am given a NxN symmetric matrix P ( P[i,i]=0, i=1...N and P[i,j]>0 for i!=j) which stands for the relative distances of N points. I would like use it to get the coordinates of the N points in a 2D plane. Of course, the solution is not unique (given one solution, I can translate or rotate all the points by the same amount and generate

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?

Apologies for the previous mail (I sent it off too early by mistake). This is the correct example: rm(list=ls()) D_mean<-seq(-5,5,length=100) y<-exp(-D_mean^2/5) pdf("my.pdf") plot(D_mean,y,type="l",yaxt="n",lty=2,lwd=2,col="black", ylab = list(expression(paste(dN/dlogD[agg]," ["*cm^-3*"]"))), xlab = expression(paste(D[agg],"

Dear All, I am given some data to analyze. The data is in the form of a Stata database (.dta file). What is the best way to import it into an R dataframe? Is there any particular caveat I should be aware of? Many thanks Lorenzo

Hello R-helpers I want to put a color scale in a plot: I've got an xy plot where the values of the response (z=f(x,y)) is symbolically given by colors (like heat or rainbow color scale) I would like to put such a scale with apprpriates labels in the plot, so as to facilitate the interpretation (like in a finite elements result plot) How is taht possible? Thanks Anne [[alternative

Dear All, I implemented an algorithm for (uniform) random rotations. In order to test it, I can apply it to a unit vector (0,0,1) in Cartesian coordinates. The result is supposed to be a set of random, uniformly distributed, points on a sphere (not the point of the algorithm, but a way to test it). This is what the points look like when I plot them, but other then eyeballing them, can anyone

Dear All, Probably something very easy, but I am looking for the most efficient ways to achieve this. Consider the following snippet y<-c('a','b','c','d','e','f','g') x<-rnorm(length(y)) df<-data.frame(y,x) leading to > df$y [1] a b c d e f g Levels: a b c d e f g Now, I would like to replace levels

Hi all A slightly off topic post, but one that I think someone out there in the NUT community could probably help me with. Summer is coming, and my office at home is getting hot... helped in part by the APC 3KVA UPS I have sitting under my desk. It kicks out heat like a bar-heater, even when there is almost no load on it (idle load is one PC, one switch, one wireless AP, and thats it). It is

Dear All, I would like to use a randomForest algorithm on a dataset. The set is not particularly large/difficult to handle, but it has some missing values (both factors and numerical values). According to what I found https://stat.ethz.ch/pipermail/r-help/2005-September/078880.html https://stat.ethz.ch/pipermail/r-help/2007-January/123117.html the randomForest package has a problem with missing