similar to: heatmap

Hi, another problem on heatmaps... after generating the graph with myBlRd <- colorRampPalette(c("blue", "red")) heatmap(dataHeat[Top100, ], col=myBlRd(15)) i need to retrieve the row names' list ordered by the dendrogram. I tried with "rownames(data)[Top100]" but the list is not ordered (as i can see in the generated picture). Any tips? Tnx AZ --

Hello everybody, I'm trying to create my own color palette on R, in order to interpolate some different temperature data on different maps (daily means, seasonal means,...). I would like to create a color palette which works for each map, so I need a color palette between -40 and +40?C. Sometimes my data for one map range from -10 to +20, sometimes from 10 to 30, etc... but always between

Dear list I'm having trouble with inverting color gradation. As seen in the "rgl" example, library(rgl) example(rgl.surface) I understand that I can assign colors to heights for each point. col <- colorlut[ y-ylim[1]+1 ] # assign colors to heights for each point However, I am now trying to assign inverted colors. (top colored green, and bottom colored gray). Is there any

Hello: I have a tab delim file with 100 rows and 100 columns. I have numerical values in this table. What I want is to create an image color map with color gradation. my values range from -5 to 0. max value is 0. to acheive this, I need to convert my data.frame into matrix. I tried following : mydf <- read.table('mytable',sep='\t',header=T) mydf1 <- mydf[,2:100]

Hi, I hope to show a heatmap with thre colours, no gradation. How to specify heatmap.2 to map "green" for values less than -1, "gray" for values between -1 and 1, and "red" for values greater than 1 ? Thanks [[alternative HTML version deleted]]

http://www.nabble.com/file/p25336596/Conductivity1.jpeg I need a little help making modifications to the image included with this post. First, rather than using a linear color legend to display the output I would like to use a log-scale legend. Thus, the legend on the right would go from 1 to 1000, for example, with a classic log-scale gradation. What I hope to avoid is taking the log of the

Hi Amudhan, Please go through the following that would clarify up-gradation concerns from DHT to RIO in 4.0 1. RIO would not deprecate DHT. Both DHT and RIO would co-exist. 2. DHT volumes would not be migrated to RIO. DHT volumes would still be using DHT code. 3. The new volume creation should specifically opt for RIO volume once RIO is in place. 4. RIO should be perceived as

Hi, How do I anchor z=0 to the white color in a levelplot so that the color changes from cyan to magenta precisely as z changes from negative to positive? Also is it easy to change color scheme, say to blue/red as it's more dramatic? Is there a better function for showing heatmap with a color bar? Thanks in advance for any help, I've played with image, heatmap and levelplot a little and

On the cover of Zivot and Wang's Modeling Financial Time Series with S Plus, there is a correlation plot that seems to indicate the strength of correlation with color-coded squares, so that more highly correlated stocks appear darker red. If anybody out there is familiar with the book or understands what I am talking about, I am curious as to whether or not there is a similar function in R

Hi, I'm kinda new of the R world. I need to use the heatmap or heatmap.2 function to plot correlation values. 2 questions: - how can I specify a color palette? (would like to have a transition from blue(-1) to white(0) to red(1)) - how can I use heatmap.2 imposing a specific order (like hclust.order)? I mean, I don't want heatmap.2 to re-cluster/re-order my data but just to plot them

?rev On Jun 16, 2009, at 5:13 AM, Naoki Irie wrote: > Dear list > > > I'm having trouble with inverting color gradation. > > As seen in the "rgl" example, > > library(rgl) > example(rgl.surface) > > I understand that I can assign colors to heights for each point. > > col <- colorlut[ y-ylim[1]+1 ] # assign colors to heights for each >

Hello R-Community, I am a rookie in R and I am fascinated with the power of bio computing by R. I am analysing gene expression data from Real time PCR. I have used absolute gene quantitation to measure gene copy number in all my transcripts. All my data has been normalised them to a housekeeping gene, which is constitutive expressed. My problem is as follows. After normalising some of the genes

Hi, Can anyone tell me how to set Z-score according to my own requirement as the below code is taking as per the file entries. Any help would be appreciable. library(gplots) x=read.table("final.txt", header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=colorRampPalette(c("green","white","red"))(256), #col=greenred(75), Rowv=TRUE, Colv=FALSE, distfun = dist,

Here?s an easy one. Well, easy for those more clever than I am. I am plotting several groups and use symbols 15:25, pch <- 15:25 Sometimes, however, I need more than those and would like to have them recycled automatically so that pch[12] = pch[1]. Perhaps I can use %% or kludge up a multi-line, multi-if solution, but hope that a kind helper can suggest something more elegant. I am also

I try to use ColorRamp as ColorRampPalette (i.e. with the same gradient), but it seems there is a nuance that I've missed. pal.crp<-colorRampPalette( c("blue", "white", "red"), space = "rgb") plot(rep(0,40),pch=16,col=pal.crp(40)) # is great But, using the same gradient with colorRamp is giving erratic colors. pal.cr<-colorRamp(

does RIO improves folder listing and rebalance, when compared to 3.x? if yes, do you have any performance data comparing RIO and DHT? On Thu, Nov 2, 2017 at 4:12 PM, Kaushal M <kshlmster at gmail.com> wrote: > On Thu, Nov 2, 2017 at 4:00 PM, Amudhan P <amudhan83 at gmail.com> wrote: > > if doing an upgrade from 3.10.1 to 4.0 or 4.1, will I be able to access > > volume

Hi all, I had the need to create a colorbar considering the alpha channel of the colors, but colorRamp() and colorRampPalette() ignored the alpha argument in rgb(). So I performed some minor modifs. in their codes, as to support the interpolation using the alpha channel. I guess that those simple modifications might be useful for other people, so perhaps it would be worth to add them to

Hi, I''m using heatmap.2 to cluster my data, using the centroid method for clustering and the maximum method for calculating the distance matrix: library("gplots") library("RColorBrewer") test <- matrix(c(0.96, 0.07, 0.97, 0.98, 0.50, 0.28, 0.29, 0.77, 0.08, 0.96, 0.51, 0.51, 0.14, 0.19, 0.41, 0.51), ncol=4, byrow=TRUE)

Hello, I am using maptools for plooting geographical data. The colour of the region indicates some region dependent value (population for example). I pass the colours of the regions to the plot.Map function by defining the foreground colour: jet.colors = colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow",

On 16/04/2016 8:47 AM, Atte Tenkanen wrote: > Hi, > > How would you calculate the "mean colour" of several colours, for > example c("#FF7C00","#00BF40","#FFFF00")? > Bert answered your subject line question. Your text is asking something else: if those are colours, you don't want to treat each of them as a single integer. A