similar to: Clustering help in Heat Maps

Ok, now we have the mapping of color names to color codes (see below) and conversion to rgb (something like Ben Bolker's function), but how to convert rgb to hsv? Thanks to Brian Ripley, Peter Dalgaard and Ben Bolker Details below Regards Jens etc/colors.big maps 455 names to rgb in S syntax etc/rgb.txt maps 657 names to rgb in C syntax, but unlike colors() it has mixed upper and

HI everyone, I''m trying to assign colors to multiple lines in a graph. Problem is I don''t want to type in as many colors as there are lines....is there a way around this? In brief, I''m plotting the logratio for up to 60 samples and want a different color for each sample. Here is the code I''m using now.. Any help is greatly appreciated.. Best LT data <-

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,

I am using attributes colsep and sepwidth from heatmap.2 function, however when using larger values for sepwidth the following columns are not moved to the right but the seperator is covering the column(s) with a white bar and the column labels and ColSideColors remain at their positions, is this intended? I expected the following columns to be shifted to the right by sepwidth. Is there a way

Hi, I am using heatmap.2 of gplots to make heatmaps of my the attached file. I am giving my code for the same .. library(gplots) x=read.table("1.txt", header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust, dendrogram = c("both"), scale = c("row"), na.rm=TRUE, trace="none",

Hi, I am drawing a heat map using gplots of R package. The file (new4) is having values 0 and 1 only. library(gplots) library(marray) x=read.table("new4", header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=colorRampPalette(c("black","red"))(256), #col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust, dendrogram = c("row"), scale =

Dear list, I have done a scatter plot of multiple variables in the same graph, with different col and pch. I managed to do it with the following code but not know how to make a function of these so that next time if I want to do similar graph but with new variables, I dont have to copy the code and then change the old variables with the new ones but just call a function with the new

I'm having problems with this example, it is posted with reproduceable code below, both with the normal 0-6 scale and the desired 3-6 scale (with bars removed). How can I get the graph to have the desired 3-6 scale without removing the bars. Thanks! #Data

Hi everybody, I am wondering how i can add a "stretch" color bar / legend to a graph that uses colorBrewer to define the colors in it. I will try to explain my graph, but i also uploaded it at: ftp://ftpext.usgs.gov/pub/er/fl/st.petersburg/Monica_pal/ The file is: robcor_training_pca.pdf - i will also attach this file in case some people accept attachments. So i took apart the

hello, all. i am trying something new and am stuck. i typically go with whatever colors the pie function pops out, but i would like to customize it. please find below a sample dataset. ##TVs per household. TVs <- factor(c(rep("0", 1), rep("1", 16), rep("2", 14), rep("3", 12), rep("4", 3), rep("5", 2), rep("6", 2)))

Hello, I am currently using the polar.plot function in the plotrix package to graph data. Unfortunately, it seems that the default for the labels is to have a background color that is covering the line representing my data, making it difficult to read. Is there a way to make this label background transparent? Example: lengths <- 0:72 bearing <- seq(from=0, to=360, by=5)

I have the following R code to create a plot with two y axes. I am essentially trying to plot a price series with a volume series on the same graph. (i.e. to compare price with volume). I can label the first y axis successfully, but the problem is in labeling the 2nd y-axis. Essentially, the label never appears. It seems as though there is not enough margin on the right hand side of

###Dear R users ###I have been using SensoMineR package from CRAN for most of my work in sensory data analysis and from my usage experience, I encountered some areas for improvement and considered ###modifying the function in SensoMineR package for my personal use. I felt that it could be useful to share this to the community for enabling adoption by other users where they might require a

I'm using this code to create a heatmap of expression data and indicate a specific column of data, post clustering: #Generate heatmap: heatmapChipDx <- heatmap.2(L3data_med2, dendrogram="column",trace="none", col=redgreen(64), colsep=seps, sepcolor="yellow", sepwidth = 0.1, margin=c(5,5), scale="row", key=FALSE) I have two problems that I'm

Hello, I'm trying to learn how to use lattice and levelplot in particular. There are three elements of customizing the plots I'm stuck with: a) Is there a way to put borders around each "cell" within a level-plot. I'm trying to do something like the colsep/rowsep/sepcolor/sepwidth parameters of heatmap.2 in gplots b) Can I alter the line-width of dendrogram added

I have written a wrapper for heatmap.2 called heatmap.w.row.and.col.clust which auto-generates breaks using breaks<-round((c(seq(from=(-20 * stddev), to=(20 * stddev))))/20, digits = 2) #(stddev in this case = 2.5) This has always worked well in the past but now I am getting an error that non-finite breaks are being generated. Drilling down, it seems that my wrapper is generating finite

Hi all , I have following script to plot some data. plot( c(1,1100), c(0,15), type='n', xlab='', ylab='', ylim=c(0.1,25) , las=2) axis (1, at = seq(0,1100,50), las =2) axis (2, at = seq(0,25,1), las =2) lines( c(1,304),c(0,0),col='grey', lwd=3 ) lines( c(1,238),c(1,1),col='grey', lwd=3 ) segments(86, 0 ,270,col = "green", pch=23,

Hi, How to mark points on x axis of a graph keeping x axis as constant and changing y from y1 to y2 respectively. I want to highlight the area from y1 to y2. Any suggestions Thank you Jeet [[alternative HTML version deleted]]

Dear all, I have a set of five datasets with string, for which I need to draw the venn diagram. there are tools available to draw venn diagram online, but limited to three sets. I can also generate venn for three from limma package, but do not know how to proceed with five subsets. Help me in drawing the same any script . Thank you Khush [[alternative HTML version deleted]]

Dear All, I am newbie to R, and I wanted to plot a barplots with R and in such a way that It will also show me position which I can plot on the bar line. Here is my code that I am using to plot, > chromosome <- c(40.2, 35.6, 36.1, 29.6, 31, 29.6, 31, 29.4, 28.2, 23, 23, 28.2) >barplot (chromosome, col="purple", xlab="Oryza sativa Chromosomes", border = NA, space =