similar to: heatmap color distribution

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 all, Does anyone know of a fairly easy way to "stretch" a heatmap vertically? I've got 42 arrays and would like to be able to see as many significant genes as possible (right now I can only get 50 genes with it still being readable). In some comparisons there are several hundred significant genes. I've fiddled with the "asp" argument, but that doesn't

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) >

Using the heatmap function in mva, it seems to be hard to use different colors in the edges leading to different groups of objects, as commonly done in many heatmaps in the microarray graphics. Any suggestions? Thanks. max

Hi all, I am interested in plotting a heatmap of a set of genes. I would like the text labels of these genes to be colored red rather than black if they meet certain statistical criteria (using an if statement). I'm not sure how to change individual color labels without changing them all. Can anyone provide some insight on how to do this? Thanks in advance, Jake

Hi, I have searched for a solution but I failed to find an answer. I am hoping you may be able to help me. I have a data set where I have observations for a number of units (n =~40) over a period of time (t =~100) and I have a variable (Z) that codes a categorical variable for each observation. I want to produce a 2D plot where time is on the x-axis and units are on the y-axis. Then each block

I'm having the exact problem outlined in a previous post from 2005 - unfortunately the post was never answered: http://tolstoy.newcastle.edu.au/R/help/05/10/15055.html When running: lm2=lars(x2,y,type="lasso",use.Gram=F) I get an error: Error in if (zmin < gamhat) { : missing value where TRUE/FALSE needed ...when running lasso via lars() on a 67x3795 set of predictors. I

I'm trying to read a binary file created by a fortran code using readBin and readChar. Everything reads fine (integers and strings) except for double precision numbers, they are read as huge or very small number (1E-250,...). I tried various endianness, swap, But nothing has worked so far. I also tried on R 64 bit for linux and windows (R 2.14) and R 2.11 on windows XP 32 bit. Any help would

Dear All I want to plot a kind of figures, which can interactive with user. For example, i have a matirx which can be showed by image function. i.e. we can compare the value depend on different colors. However, the change of colors depend on the range of value. Nowaday, i want to set a bar, which can be moved by user such that the user can obtain the appropriate range. Does anyone suggest me which

Hello I'm using rainbow function to generate 10 colors for the plot and it is difficult to tell the neighboring colors from each other. How can I make the colors more differently. Thanks Zhaoming [[alternative HTML version deleted]]

This patch-series implements the ARB_viewport_array for nvc0 and does a little house-cleanig afterwords. V2: Add Release-Notes, mark this in GL3 as done for nvc0 Don't mark the scissors dirty when we don't need to do that Tobias Klausmann (3): nvc0: implement multiple viewports/scissors, enable ARB_viewport_array docs: update GL3.txt, relnotes: mark GL_ARB_viewport_array as done

Hi, I was trying to use par(mfrow) to put 4 heatmaps on a single page. However, I get one plot per page and not one page with 4 plots. What should I modify? Test code is given below: test = matrix(rnorm(60), 20, 3) pdf(file='test.pdf',width=10,height=8) par(mfrow=c(2,2)) heatmap(test) heatmap(test) heatmap(test) heatmap(test) dev.off() thanks! [[alternative HTML version deleted]]

Hi all, In heatmap's documentation, it mentions that the output value is actually an invisible list...how would one access this list? Thanks, Jake

The answer is "don't do that" because that function abuses par. Use lattice or ggplot2 with grid graphics to plot multiple heatmaps. https://stackoverflow.com/questions/15114347/to-display-two-heatmaps-in-same-pdf-side-by-side-in-r -- Sent from my phone. Please excuse my brevity. On July 23, 2017 5:11:32 AM PDT, Brian Smith <bsmith030465 at gmail.com> wrote: >Hi, >

This patch-series implements the ARB_viewport_array for nvc0 and does a little house-cleanig afterwords. Tobias Klausmann (3): nvc0: implement multiple viewports/scissors, enable ARB_viewport_array nvc0: mark scissor in nvc0_clear_{} nv50/ir: Remove NV50_SEMANTIC_VIEWPORTINDEX and its last consumer .../drivers/nouveau/codegen/nv50_ir_driver.h | 1 -

Hello! I looked for help through google and the help-files and spend several hours with trial and error, but didn't find a correct way. It's all about lines in a heatmap to separate different data block from each other to underline the significance of the found clusters! The heatmap is build like that: heatmap(X, Rowv=NA, Colv=NA, symm=TRUE, cexRow=0.3, cexCol=0.3) I switched the

Hi, I have some data which I was plotting using image(). I wanted to add a vertical color key to the plot and I found that heatmap.2 in gplots does let me add a color key. However, I was thinking of a vertical bar with the color range rather than the style that gplots provides. Is there any package (or code snippet) that would let me add a vertical color key to an image() or heatmap

I would like to use gridBase to place four separate heatmaps (actually, a stripped-down heatmap.2 from ght gregmisc package that contains only the "image" part) into four different viewports. I can get the placement correct, but I keep 'losing' the previous plot. Any suggestions? Here is some quick example code trying to put a heatmap into the left viewport and then

Using the small reproducible example below, I'd like to know if one can somehow use the matrix "sig" (defined below) to add a black outline (with lwd=2) to all pixels with a corresponding value of 1 in the matrix 'sig'? So for example, in the ggplot2 plot below, the pixel located at [1,3] would be outlined by a black square since the value at sig[1,3] == 1. This is my first

Functionally identical but much simpler. Should also better integrate with future layer/viewport changes/fixes. Cc: 10.1 <mesa-stable at lists.freedesktop.org> Signed-off-by: Ilia Mirkin <imirkin at alum.mit.edu> --- Not *strictly* necessary in stable, but it will make backporting later fixes easier. No regressions in piglit. src/gallium/drivers/nouveau/nv50/nv50_program.c | 5