similar to: Howto fix colors in colorRampPalette?

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, 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

Try: n = 100; x = matrix(seq(-10, 30, length.out=500), ncol=1) col = colorRampPalette( c("green", "white", "red"), space="rgb")(n) breaks = c(seq(-10, 0, length.out=n/2)-0.5, 0, seq(0, 30, length.out=n/2)+0.5) image(x, col=col, breaks=breaks) See also today's discussion on R-Help about "red-black-green color palette", since most of the

I will second Roger's suggestion, colorRampPalette is a great function for creating your own palettes. For example, Matlab's jet palette (also available in fields package under peculiar name 'tim.colors') can be defined by: jet.colors = colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow",

I'm working on some heatmaps, and the person I'm working with would prefer a red-black-green color palette (red denoting gene induction and green denoting gene repression). Does such a palette exist already? If not, is there an easy way to create one? Thanks, Jake

Hi, I am trying to create a heatmap with some specific requirements. Specifically, I need to be able to center the color-scale around 0, and I need to truncate the data so that a few extreme values do not cause the rest of the heatmap to appear black (on a red/green scale). After reading through and experimenting with heatmap, heatmap.2, heatmap_plus, and heatmap_2, I believe heatmap.2 will

Dear R users, I am trying to print heatmaps in a loop (with a pause). Idea is to visualize changing correlations over time and for testing I wrote this simple (reproducible) code below. My problem is that levelplot() does not produce any output when I run the code (though heatmap does). Ideally I would like to use levelplot() as it produces a neat index on the side indicating the color and the

Dear List, I am trying to get a basic plot to show a continuous range of fill colors. It is probably easiest to demonstrate. I would like a legend like in the following example: Satellite.Palette <-colorRampPalette(c("blue3","cyan","aquamarine","yellow","orange","red")) require(fields) image.plot(volcano, col = Satellite.Palette

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 --

Hi, I have a matrix with both positive and negative numbers, I would like to use image() to draw a heatmap. How can I can design a palette (or is there a function already available) that treat negative numbers in a blue gradient and positive numbers in a red gradient and treat 0 as white? Thanks

Hi I made heatmap of QTL based on Lod score. Where I have traits in columns and marker data (rows). I can not cluster both column and rows as I need the right order for marker data. Can someone suggest me better way of generating heatmaps especially the colour key I want to select to visualize the results which are more interesting to look at. > library(gplots) >

Hello there! I'd just like to say in advance, "Thank you," for any help and/or advice. My problem is as follows: I have a dataset that is made up of percentages. I've assigned my "error" percentages a value of '-100', my "non-existent" percentages a value of '0', and all my other percentages are normal values that range from the high

Hello R-Users! I'm using a heatmap to visualize a matrix of values between -1 and 3. How can I set the colors so that white is zero, below zero is blue of increasing intensity towards -1 and above zero is red of increasing intensity towards red? I tried like this (using the marray and gplots packages from bioconductor): mcol <- maPalette(low="blue", mid="white",

Hm..., Should these two versions produce the same solution? Unfortunately and shame to confess, I don't know much about the colors in R: myColors <- c("#FF7C00","#00BF40","#FFFF00") Colors=rgb2hsv(col2rgb(myColors)) apply(Colors,1,mean) h s v 0.2122974 1.0000000 0.9163399 * * * * * # Average the 1st two by taking the middle colour

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(

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

Hello, I have two questions. I'd like to visualize data with a heatmap and I have the following testcase: x <- rnorm(256) nx <- x + abs(min(x)) nnx <- 255/max(nx) * nx x <- matrix(nnx, 16, 16) rownames(x) <-

On 16/04/2016 12:33 PM, Atte Tenkanen wrote: > Hm..., > > Should these two versions produce the same solution? I wouldn't expect them to. Duncan Murdoch Unfortunately and > shame to confess, I don't know much about the colors in R: > > myColors <- c("#FF7C00","#00BF40","#FFFF00") > Colors=rgb2hsv(col2rgb(myColors)) >

Hi everyone, I wanted to draw your attention to a new post on the developer.R-project.org blog: https://developer.R-project.org/Blog/public/2019/04/01/hcl-based-color-palettes-in-grdevices/ A new function grDevices::hcl.colors() greatly extends the color palette functionality available in base R. Also, the defaults in the heatmap functions image() and filled.contour() have been adapted

Hello, I am trying to plot SADIE red-blue plots of cluster indicies using filled.contour. I want a plot which only has three bins for the data: <-1.5, -1.5 - 1.5, >1.5, but I am having trouble getting there. example X1 X2 X3 X4 X5 1 -5 -4.5 1.0 4.5 6 2 -3 -2.0 1.2 -1.0 3 3 0 0.0 0.0 -0.5 -1 4 -2 -3.0 1.0 1.5 3 5 -6 -2.0 0.5 3.0 2 example<-as.matrix(example)