Re: [R] heatmap ploting

Hi Steve, That plot looks to me as though a value-to-color transformation is performed on the logarithm of gene expression. The scale bar can be roughly reproduced like this: library(plotrix) plot(0,xlim=c(0,3)) gradient.rect(0,-0.1,3,0.1, col=color.scale(seq(0,3,0.1), c(0.7,1,1,1,0.7,0.2),

[R] heatmap ploting

Dear Community, I have an example heatmap plot in this link which was generated by java I believe, I want to make a similar plot in R. Any clues on how to do it? Thanks. The column is a gene, and the rows are

Re: [R] Heatmap

Hello, Just do col = rev(heat.colors(256)) ? Hope this helps, Rui Barradas Às 12:55 de 21/10/19, Eleftheria Dalmaris escreveu: Hello all, I have made the attached heat map without a problem. On this heat map, the yellows are my high values and the oranges are my low values. Is there a way

[R] Heatmap

Hello all, I have made the attached heat map without a problem. On this heat map, the yellows are my high values and the oranges are my low values. Is there a way to change that? Where the orange color is to have the yellow and vice versa? Thanks a lot, Eleftheria P.S. In case is needed here

Re: [R] heatmap.2, adding a legend at bottom

ot;Legend", xpd=TRUE) David L Carlson Department of Anthropology Texas A University College Station, TX 77843-4352 -Original Message- From: R-help On Behalf Of Ding, Yuan Chun Sent: Thursday, October 4, 2018 1:19 PM To: r-help@r-project.org Subject: Re: [R] heatmap.2,

Re: [R] heatmap.2, adding a legend at bottom

ot;Legend", xpd=TRUE) David L Carlson Department of Anthropology Texas A University College Station, TX 77843-4352 -Original Message- From: R-help On Behalf Of Ding, Yuan Chun Sent: Thursday, October 4, 2018 1:19 PM To: r-help@r-project.org Subject: Re: [R] heatmap.2, adding a lege

Re: [R] heatmap.2, adding a legend at bottom

Hi All, I generated the attached heatmap using the following R code and attached testfile. I tried to move the legend to the bottom, Can anyone help me? I have played for 3 hours and can not resolve the problem. I realized that in the last email, I forgot to include the "Group" variable

[R] heatmap.2, adding a legend at bottom

Hi All, I generated the attached heatmap using the following R code and attached testfile. I tried to move the legend to the bottom, Can anyone help me? I have play for 3 hours and can not resolve the problem. Thank you, Ding

Re: [R] Heatmap help

Hi, you have a couple of things going on here. You can reorder your matrix by creating an index like this: > A_index=c(grep(".A", colnames(A)), grep(".B", colnames(A))) and do this: > heatmap.2(A[,A_index], dendrogram="col", Rowv = colnames(A)[A_index], > tracecol =

Re: [R] Heatmap help

Thanks, Patricia! I will do it by the rows, and your explanations were great and easy to follow! Thank you very much for your help and time. Andre On Mar 4, 2017 4:18 PM, "Patricia J. Hawkins" wrote: Hi, you have a couple of things going on here. You can reorder your

[R] Heatmap help

Dear all, I was wondering if you could help me to construct a heat map, in which the columns are sorted by sample type (A first and then B). My reproducible example below runs, but the columns of the heatmap are not organized in the way I would like because it has first sampleA, SampleB, sampleA,

Re: [R] Heatmap Colnames

Hi Nils, I don't have the GMD library, but this looks like some axis labels are being ignored to avoid overlapping. If heatmap.3 uses base graphics you can probably get your labels by passing empty strings to heatmap.3 and then displaying the axis with staxlab (plotrix). Jim On Wed, Apr 6, 2016

[R] Heatmap Colnames

Hello, please see below my code for a heatmap. Unfortunately my column names do not completely appear. Can you please send me the appropriate code to visualise them? Many Thanks! Nils library(GMD) dat<-data.frame(EntryA=as.numeric(c(4.24,3,1.66,1.28,1.2,-1.32,-1.88)),

Re: [R] Heatmap.2 error

Pijush, The error is a result of you having repeated color values. The warnings can be addressed by changing the arguments that you use. Attachments are removed from posts to R Help, so I used different data to show you an example. Jean library(gplots) data(mtcars) x -

[R] Heatmap.2 error

Dear Sir, Please help me solving the error occurring during the execution of the code given below. library(openxlsx) library(gplots) library(RColorBrewer) rix - read.xlsx(file.choose(), sheet = 1, colNames = TRUE,rowNames = TRUE) rawdata - data.matrix(rix) colors =

Re: [R] Heatmap

On May 22, 2015, at 10:32 AM, Carlos Javier Rincon Rodriguez wrote: Hi. Good morning. I am trying to load a shapefile to do a heatmap of Colombia. I using all this package: library(ctv) library(spatial) library(ggplot2) library(sp) library(rgdal) library(rgeos)

Re: [R] Heatmap

Hi Carlos, The error from: readShapePoly(depto.shp) may well be that the function cannot find the file. Assuming that there is a file depto.shp, is it in the working directory of R when you issue this command? Find out by: getwd() I suppose that macintosh computers try to hide the actual

Re: [R] Heatmap

Hi. Good morning. I am trying to load a shapefile to do a heatmap of Colombia. I using all this package: library(ctv) library(spatial) library(ggplot2) library(sp) library(rgdal) library(rgeos) library(maptools) library(ggmap) and a using this two commands to load the file:

Re: [R] Heatmap

Look at the heatmap function John David Sorkin M.D., Ph.D. Professor of Medicine Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology and Geriatric Medicine Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore,

[R] Heatmap

Dear all, I need to make a heapmap of SPI results for a monthly timeseies of 30 years. Does anybody know to do it? Thanks for your help John [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and

Re: [R] Heatmap - strange horizontal lines

I don't use these functions often enough to know their idiosyncrasies, but they appear to treat zero like a NA, and your second file has lots of zeros. I suspect this is due to the default way the continuous act data are 'cut excluding the left side of the bins. If you read the help files you

[R] Heatmap - strange horizontal lines

Dear list, I would like to make heatmaps from my data. Acctualy, I have already done it, but the issue it that is doesn't work well for all files. All files have the same structure, after importing them I do few calculations using the same script, to obtain variables for plotting. You can find

[R] heatmap indexing x axis and y axis

Dear all , I plotted a heat map of 20*20 matrix (lets say x axis and y axis comprises of alphabets A,D.G and so on) which contain multiple values for each entry in the dataset. I need to rearrange x axis and y axis on the basis of similar properties on x axis and y axis such as A E,H and

[R] Heatmap, and heatmap.2 gave different figures for the same dataset

I have a huge dataset(15k X 18) and tried to use the heatmap in R to examine the patterns. However, I found that heatmap and heatmap.2 gave me completely different outputs. Here are the codes: dim(as.matrix(data.dcpm)) [1] 15462    18 heatmap(as.matrix(data.dcpm),

Re: [R] Heatmap, and heatmap.2 gave different figures for the same dataset

Read the help page for both and pay particular attention to the scale argument. Kevin Wright On Thu, Dec 12, 2013 at 9:45 AM, capricy gao capri...@yahoo.com wrote: I have a huge dataset(15k X 18) and tried to use the heatmap in R to examine the patterns. However, I found that heatmap and

Re: [R] Heatmap, and heatmap.2 gave different figures for the same dataset

Thank you very much for the hints. I fixed the problem. On Thursday, December 12, 2013 2:08 PM, Kevin Wright kw.s...@gmail.com wrote: Read the help page for both and pay particular attention to the scale argument. Kevin Wright On Thu, Dec 12, 2013 at 9:45 AM, capricy gao

[R] Heatmap Help

Hello, I want a help, i have to make heat map.And i am using the following command In R for generating a matrix, but its returning an error,and i am not able to figure it out. Can you please tell me what is wrong? And please also suggest me how to generate a heat map. Its very urgent. Thanks a

Re: [R] Heatmap Help

You have some randomly doubled quotation marks and parentheses. A text editor with syntax highlighting is wonderful for catching that sort of problem. Beyond that, see: ?heatmap A very urgent request suggests homework to me, which this list doesn't do. Though sometimes someone will offer a

[R] Heatmap with mouseover

Dear all, what is the recommended way to create heatmaps (or plots in general) with mouseover-effect in R, so that I can embed it into a web app? Options I have found so far are a) rCharts or b) sendplot. What are your experiences and recommendations? Thanks Andreas [[alternative HTML

Re: [R] heatmap scale parameter question

I do not want to use the b word, but can anyone who also subscribes to the r-developer list forward my observation regarding heatmap? I am pretty confident that the behaviour of heatmap in R 3.0.1 is not that one intended. On 31 July 2013 14:03, Witold E Wolski wewol...@gmail.com wrote: Would

[R] heatmap scale parameter question

Would anyone of the more experienced r-users explain to me the behaviour of the scale parameter in the heatmap function. different options for scale (R 3.0.1) do change only the colors but do not affect the dendrograms. Please see for yourself executing the following code: d -

Re: [R] heatmap scale parameter question

Texas AM University College Station, TX 77840-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Witold E Wolski Sent: Wednesday, July 31, 2013 7:04 AM To: r-help@r-project.org Subject: [R] heatmap scale parameter question Would

[R] heatmap scale parameter

does change only the colors but dendrograms are unaffected. d - matrix(rnorm(100),nrow=20) heatmap(d) heatmap(d,scale=column) heatmap(d,scale=row) heatmap(d,scale=none) However scaling clearly affects clustering. see: d - scale(d) heatmap(d,scale=none) R version 3.0.1 (2013-05-16) -- Good

Re: [R] Heatmap with error message: `x' must be a numeric matrix

On Jun 25, 2013, at 21:51 , Rui Barradas wrote: Hello, Your data has commas as decimal points, R uses the period. So the data is read in as strings, not numbers. You can change this by using argument 'dec' of read.table: ?read.table read.table(...etc..., dec = ,) Or you can

[R] Heatmap with error message: `x' must be a numeric matrix

Hi I am trying to do a heatmap, but I can't see what I am doing wrong. I get the error message: `x' must be a numeric matrix, but as far as I know I have changed my data into a matrix. The dataset I have in my example of my run is only a small part. I have around 1000 rows in total. I have

Re: [R] Heatmap with error message: `x' must be a numeric matrix

Hello, Your data has commas as decimal points, R uses the period. So the data is read in as strings, not numbers. You can change this by using argument 'dec' of read.table: ?read.table read.table(...etc..., dec = ,) Or you can replace the commas with periods: data[] - sapply(data,

[R] Heatmap missing in Heatmap.2 output

Hi, I have a matrix 11x7761245 and I am trying to do clustering, dendrogram and heatmap. The analysis was completed but only the dendrogram was written in the jpeg file. The heatmap was missing. May I know if anyone know this problem? My script: hc = hclust.vector(x, method=ward) dend =

[R] heatmap tile size question

Hello List I was wondering if it is possible to make the individual 'tiles' in a heatmap larger. Often when I plot heatmaps and want to label the rows with eg gene names I either have to shrink the text or leave it out altogether as it becomes so small as to be unreadable. I wondered if there

Re: [R] heatmap.2 problem

On 12.01.2013 23:40, Peter Davidsen wrote: Dear List, I'm trying to generate a simple heatmap that has each row and column separated by a black line. However, for some reason this only happens for the first and last color. The middle color in my colorpanel() command has an addition horizontal

Re: [R] heatmap.2 problem

Sorry, I should have added library(gplots) in the beginning of my code On Sun, Jan 13, 2013 at 5:04 PM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: mycol - colorpanel(n=3,green,grey,red) - - - Peter K Davidsen | MSc, PhD stud. | Centre for Systems Biology | Univ. of Liverpool |

[R] heatmap.2 problem

Dear List, I'm trying to generate a simple heatmap that has each row and column separated by a black line. However, for some reason this only happens for the first and last color. The middle color in my colorpanel() command has an addition horizontal and vertical line that I would like to get rid

Re: [R] heatmap with symbols

Use the col= argument to the heatmap() function to specify the three colors you want. For example: x - matrix(rnorm(50), ncol=5) heatmap(x, col=1:3) Jean furor furor1...@gmail.com wrote on 11/14/2012 03:31:42 AM: Hi all, I've made a heatmap using '-', '=' and '+' as

[R] heatmap with symbols

Hi all, I've made a heatmap using '-', '=' and '+' as possible values. However, the heatmap itself shows more than three colors. How to avoid this? Thanks in advance. regards -- View this message in context: http://r.789695.n4.nabble.com/heatmap-with-symbols-tp4649472.html Sent from the R

Re: [R] Heatmap Colors

On Fri, 28 Sep 2012, David Winsemius wrote: On Sep 28, 2012, at 4:52 PM, David Winsemius wrote: On Sep 28, 2012, at 3:16 PM, Nick Fankhauser wrote: 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

[R] Heatmap Colors

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

Re: [R] Heatmap Colors

On Sep 28, 2012, at 3:16 PM, Nick Fankhauser wrote: 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

Re: [R] Heatmap Colors

On Sep 28, 2012, at 4:52 PM, David Winsemius wrote: On Sep 28, 2012, at 3:16 PM, Nick Fankhauser wrote: 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

[R] Heatmap : Export data after clustering

Dear all, I'm currently using the gplots plug-in for R to make a clustered heatmap and I'm wondering if there is any possibility to export the clustered data ? (basically to get an excel table with the raw data reordered according to the clustering). I'm sorry if this question seems a bit

[R] heatmap.2 clustering and adding add.expr

Hi , I am trying to plot a heatmap with a correlation matrix and trying to highlight significant correlations . i am using my matrix d874n has 78 columns ex2-corAndPvalue(data.matrix(d874n),use = pairwise.complete.obs) ##creating a matrix of true false using p values sig-ex2$p0.05 nx=78 ny=78

[R] heatmap

Dear all, I have a data set which is 100 \times 100 matrix. I made a heatmap of the data. The xlim and ylim are both shown to be c(0,1). I want to make both the xlim and ylim to be c(0,100). So the heatmap correspond to the 100 \times 100 locations. Thank you. Hannah

Re: [R] heatmap

On May 13, 2012, at 11:23 AM, li li wrote: Dear all, I have a data set which is 100 \times 100 matrix. I made a heatmap of the data. The xlim and ylim are both shown to be c(0,1). I want to make both the xlim and ylim to be c(0,100). So the heatmap correspond to the 100 \times 100 locations.

[R] Heatmap fidelity

I'm having a problem when using heatmap. Even though the diagonal of my matrix is all the same value, the diagonal of my heatmap is not all the same color. Any suggestions? Here is some reproducible code: # # Get data nba -

Re: [R] Heatmap fidelity

On 26/04/2012 9:01 AM, Steven Wolf wrote: I'm having a problem when using heatmap. Even though the diagonal of my matrix is all the same value, the diagonal of my heatmap is not all the same color. Any suggestions? heatmap() rescales the matrix by default. Use heatmap(abs(psim),

Re: [R] Heatmap fidelity

Thanks! -Steve -Original Message- From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] Sent: Thursday, April 26, 2012 9:28 AM To: Steven Wolf Cc: r-help@r-project.org Subject: Re: [R] Heatmap fidelity On 26/04/2012 9:01 AM, Steven Wolf wrote: I'm having a problem when using heatmap

[R] heatmap.2 (blurred output heatmap)

Hi I used to make heatmaps using following commands but now some thing has changed as I get library(gplots) heatmap. 2(qtl.map,Rowv=F,dendrogram=column,col=colorRampPalette(c(blue,lightblue,black,black,yellow,red)),breaks=seq(-4.01,4.01,length.out=51), density.info=none, ) following error and

Re: [R] heatmap.2 (blurred output heatmap)

example(heatmap.2) works for me, hence it is either your data, your version of some package or your version of R that causes the problems, we do not have information of any of these although the posting guide asks you to provide this for each posting. So we cannot help. Uwe Ligges On

[R] heatmap for plotting categorical matrix

Hi there, I have a matrix like this: a4[1:20, 1:5] 194 211 294 314 315 GO:003 1 1 1 1 1 GO:072 0 0 0 0 0 GO:076 1 0 0 0 0 GO:082 1 3 1 1 1 GO:083 1 0 0 0 1 GO:086 0 1 0 1 1 GO:114 0 0 0 0

Re: [R] heatmap for plotting categorical matrix

not sure about gplots, but the one in base R should work well if you specify the scaling method to be 'none': heatmap(a4[1:40, ], Rowv=NA, Colv=NA, col=c(grey, blue, purple, red), scale='none') Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department

[R] heatmap

Dear R users, need help with my heatmap. I will really approciate some help. Given the matrix: head(x) A B C D time [1,] 0 8 0 01 [2,] 0 160 0 02 [3,] 0 175 0 03 [4,] 0 253 0 04 [5,] 79 212 0 05 [6,] 6 105 0 06 and call: ## Heatmap

[R] heatmap.2 with colsep and sepwidth

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

[R] heatmap

Hi everyone, I have three numerica vectors: x, y, z. I want to plot a heatmap or surface plot of z against x and y. Is there any package for this? If possible, please drop me several lines of example code. Thanks! jinrui, __ R-help@r-project.org

Re: [R] heatmap

You mean like the examples in help(heatmap) ? On Tue, Sep 6, 2011 at 1:20 PM, Jinrui Xu jinru...@umich.edu wrote: Hi everyone, I have three numerica vectors: x, y, z. I want to plot a heatmap or surface plot of z against x and y. Is there any package for this? If possible, please drop me

Re: [R] heatmap

Hi Sarah, To me, the heatmap function calculates density value for each grid of the heatmap automatically from the input matrix. In my case, I already got the density value as a vector, say Z. I want to plot a heat map with x and y as is axsis and z values as the density of grid. I am

Re: [R] heatmap

I wrote this function (borrowing heavily from an example from Longhow Lam) heatplot = function(x,y,z,bgcol=#777044,coltype='heat', ccex = 1.5, circles=TRUE, ...){ #browser() layout(matrix(c(1, 2, 3), nc=3), widths=c(7, 1, .5)) ## create the scatterplot withdifferent colors

Re: [R] heatmap is producing unwanted horizontal and vertical lines?

Sent: Monday, 8 August 2011, 14:37 Subject: Re: [R] heatmap is producing unwanted horizontal and vertical lines? Hi Col, Without seeing your data and the heatmap you are plotting it is hard to tell what is going on. Are the NAs in any pattern? NAs appear in heatmap as the background colour

Re: [R] heatmap is producing unwanted horizontal and vertical lines?

morga...@cardiff.ac.uk; r-help@r-project.org r-help@r-project.org Sent: Tuesday, 9 August 2011, 1:32 Subject: Re: [R] heatmap is producing unwanted horizontal and vertical lines? Is it this? https://stat.ethz.ch/pipermail/r-devel/2011-July/061540.html Try a recent version of R 2.13.1 patched

[R] heatmap is producing unwanted horizontal and vertical lines?

Hello, I must start by saying that I am an R novice and am sorry if this is a no-brainer... I have an csv file that contains a grid of 300x300 data points. Each point represents a 1Km square on a map. Each point is either a floating point number or NA. I load the data in with:   data -

Re: [R] heatmap is producing unwanted horizontal and vertical lines?

col_f...@yahoo.com Sent: Monday, 8 August 2011, 14:37 Subject: Re: [R] heatmap is producing unwanted horizontal and vertical lines? Hi Col, Without seeing your data and the heatmap you are plotting it is hard to tell what is going on. Are the NAs in any pattern?  NAs appear in heatmap

Re: [R] heatmap is producing unwanted horizontal and vertical lines?

to be productive: white lines anti-aliasing pdf (or variations there within) -- David Best regards, Col. From: Peter Morgan morga...@cardiff.ac.uk To: Colin Ford col_f...@yahoo.com Sent: Monday, 8 August 2011, 14:37 Subject: Re: [R] heatmap is producing unwanted horizontal

Re: [R] heatmap is producing unwanted horizontal and vertical lines?

without the white lines going through but just cant seem to find a way to do that? Best regards, Col. From: Peter Morgan morga...@cardiff.ac.uk To: Colin Ford col_f...@yahoo.com Sent: Monday, 8 August 2011, 14:37 Subject: Re: [R] heatmap is producing unwanted

[R] heatmap with RNA-Seq data

Hi all, new to this forum I'm try to using R to draw a heatmap of my RNA-seq data before doing that I did a log2 transformation of my data and produce a lot -inf in the matrix when I try to use the heatmap function, it seems can not deal with the -inf so I was wondering how to deal with these

Re: [R] heatmap with RNA-Seq data

On Jul 18, 2011, at 3:34 PM, rebioman wrote: Hi all, new to this forum I'm try to using R to draw a heatmap of my RNA-seq data before doing that I did a log2 transformation of my data and produce a lot -inf in the matrix when I try to use the heatmap function, it seems can not deal with

Re: [R] heatmap with RNA-Seq data

That what I did, I replaced the -infinite with lowest number I got from my data set. I'm not sure this kind of data manipulation is allowed in a publication -- View this message in context: http://r.789695.n4.nabble.com/heatmap-with-RNA-Seq-data-tp3676207p3676280.html Sent from the R help

Re: [R] heatmap with values

On 06/14/2011 08:53 PM, Agustin Lobo wrote: Hi! I'm displaying a contingency table with heatmap(): svm.predPix.tabla svm.predPix CC DD LL NN NN2 CC 22 0 3 8 3 DD 0 27 0 1 0 LL 1 1 90 3 7 NN 2 0 1 11 4 NN2 0 0 5 1 20

Re: [R] Heatmap in R and/or ggplot2

On Tue, Jun 14, 2011 at 19:56, idris idris.r...@gmail.com wrote: Follow up question: My data contains x, y, height, and day. I want to create the heatmap for each day, keeping the color coding consistent. I've created an example with 2 days, and you can see the charts below. Notice that

Re: [R] Heatmap in R and/or ggplot2

Thanks for the tip on the limit attribute on scale_fill_gradientn. I'll check out mencoder and let you know if I use your code for the movie. Cheers -- View this message in context: http://r.789695.n4.nabble.com/Heatmap-in-R-and-or-ggplot2-tp3594590p3600034.html Sent from the R help mailing

[R] heatmap with values

Hi! I'm displaying a contingency table with heatmap(): svm.predPix.tabla svm.predPix CC DD LL NN NN2 CC 22 0 3 8 3 DD 0 27 0 1 0 LL 1 1 90 3 7 NN 2 0 1 11 4 NN2 0 0 5 1 20 heatmap(svm.predPix.tabla[5:1,], Rowv=NA,

Re: [R] Heatmap in R and/or ggplot2

Thanks for your help! Follow up question: My data contains x, y, height, and day. I want to create the heatmap for each day, keeping the color coding consistent. I've created an example with 2 days, and you can see the charts below. Notice that the legend changes from day 1 to day 2. How can I

[R] Heatmap in R and/or ggplot2

I have a dataframe df with columns x, y, and height. I want to create a heatmap-like plot that creates a grid of x by y, and then color codes the grid depending on the value of height. Is there a ggplot2 object to do this? I'm able to easily do this in Excel with pivot tables and conditional

Re: [R] Heatmap in R and/or ggplot2

Hi, Try this ggplot(df, aes(x,y)) + geom_tile(aes(fill=height), colour=white) + scale_fill_gradientn(colours = c(red, gold, green)) + geom_text(aes(lab=height)) HTH, baptiste On 14 June 2011 07:12, idris idris.r...@gmail.com wrote: I have a dataframe df with columns x, y, and height. I want

Re: [R] heatmap question

Yes I understand what ?text means, I meant is it possible to use this function (as an argument) with heatmap.2, but I learned I can use add.expr=mtext() to do that. However I'm not simply trying to add more text to the graph but rather move the display of the x-axis labels from the

Re: [R] heatmap question

On Jun 3, 2011, at 9:26 AM, Mark Aquino wrote: Yes I understand what ?text means, I meant is it possible to use this function (as an argument) with heatmap.2, but I learned I can use add.expr=mtext() to do that. However I'm not simply trying to add more text to the graph but rather

Re: [R] heatmap question

Brilliant, that's exactly what I needed. Thank you. The axis labels are duplicated on top and the bottom now though, but I'm sure there's a way to suppress them from appearing. On Jun 3, 2011, at 11:24 AM, David Winsemius wrote: On Jun 3, 2011, at 9:26 AM, Mark Aquino wrote: Yes I

[R] heatmap question

Hi, I have what would seem to be a very simple problem but have been unable to find any way to go about solving it: I am using heatmap.2 to create a heatmap and by default the x axis label is at the bottom of the heatmap, I simply want to move the label to the top of the heatmap. Any help

Re: [R] heatmap question

On Jun 2, 2011, at 4:08 PM, Mark Aquino wrote: Hi, I have what would seem to be a very simple problem but have been unable to find any way to go about solving it: I am using heatmap.2 to create a heatmap and by default the x axis label is at the bottom of the heatmap, I simply want to

Re: [R] heatmap.3

I am intesrested by your heatmap function (allowing matrix in ColSideColors option). Can you give your complete code of your function? thanks -- View this message in context: http://r.789695.n4.nabble.com/heatmap-3-tp1566584p3498156.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] heatmap.2 - change column row locations; angle / rotate

Hi Chakravarthy, [dont forget to Cc the list for useRs with the same Q.] If you're trying to reuduce the isze of your row or column labels, i think the following arguments of heatmap.2 {gplots} is what you want to adjust- 'cexCol' and 'cexRow'. Specifically on my question that you ask

[R] heatmap clustering dendrogram export

Hi, I am a beginner for R. I had use gplots to generate a heatmap as following: heatmap.2(matrix, col=topo.colors(75), dendrogram=column, Rowv=FALSE, trace=none, key=TRUE, keysize=0.8, density.info=none, cexRow=0.2, cexCol=0.6) It work well. It generate heatmap whith rcolumn clustering

[R] heatmap clustering dendrogram export

To: r-help@r-project.org Date: Mon, 11 Apr 2011 11:15:52 +0200 Subject: [R] heatmap clustering dendrogram export Hi, I am a beginner for R. I had use gplots to generate a heatmap as following: heatmap.2(matrix, col=topo.colors(75), dendrogram=column, Rowv=FALSE, trace=none, key=TRUE, keysize=0.8

[R] heatmap cluster

Hi all, I am new to heatmap function in stats package, so any advice will be greatly appreciated. So I have a dataset that I want to draw a heatmap, for example: dput(a) structure(c(-8.256023, -14.764429, -10.145779, -5.123104, -11.974729, -16.329029, -16.329029, -16.329029, -2.764114,

[R] heatmap-how to change the order of the rows (genes)

Hi, I have a question about the heatmap dendrogram in R. I loaded my data matrix in command heatmap(), and it gave me a heatmap accordingly, and the rows (genes) also were clustered accordingly. But now I don't want the genes clustered in that way, I have a new order of these genes, and want

Re: [R] heatmap-how to change the order of the rows (genes)

the genes clustered in that way, I have a new order of these genes, and want the rows of the heatmap are drawed as the order I give.  Could anybody help me on that?  Thank you! Check out the docs for heatmap a bit more carefully: R ?heatmap I would try setting Rowv=NA, and reorder the rows

Re: [R] heatmap-how to change the order of the rows (genes)

Date: Wed, 9 Feb 2011 12:18:57 -0500 From: yanliu...@gmail.com To: r-help@r-project.org Subject: [R] heatmap-how to change the order of the rows (genes) Hi, I have a question about the heatmap dendrogram in R. I loaded my data matrix in command

[R] heatmap.2

Dear List! I'm using R2.8.1 with windows. In my Analysis I use the heatmap.2 function. That works quite well except there is one little detail I can't change. I like to make the key a bit smaller than default. So I pass in keysize=1 into the function. The key is smaller, but the main and the x y

[R] heatmap/clustering/corelation/sameorder

Hi I am trying to make heatmaps first based of QTLs profile only and then I want to cluster them based on Column only!!! Expression QTLs heat map heatmap.2(expression.qtl,Rowv=F,dendrogram=column,trace=none, distfun = function(c) as.dist(1 - c), density.info=none, trace=none, cexRow = .65,

Re: [R] Heatmap construction problems

It's hard to know without a minimal reproducible example, but you probably want scale_fill_gradient or scale_fill_gradientn. Hadley On Thu, Oct 28, 2010 at 9:42 AM, Struchtemeyer, Chris stru...@okstate.edu wrote: I am very new to R and don't have any computer program experience whatsoever.  I

[R] Heatmap construction problems

I am very new to R and don't have any computer program experience whatsoever. I am trying to generate a heatmap of the following data: Phylum,AI,AJT,BY,GA,Grt,Sm Acidobacteria,0.5,0.7,2.7,0.1,2.6,1.0 Actinobacteria,33.7,65.1,9.7,2.0,3.9,2.1 Bacteroidetes,9.7,5.6,0.7,13.2,41.1,21.6

[R] heatmap

Hi All Has anyone used correlation (Pearson or cosine or others) for clustering in heatmaps? If so, could you please tell me how? Thanks Leila __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the

Re: [R] Heatmap/Color Selection(Key)

Hi Rashid, you may have a look at the colorRampPalette-function, along with the at argument oh heatmap.2 x-matrix(runif(100,-6,6),nrow=10) heatmap.2(x,col=colorRampPalette(c(blue,lightblue,darkgray,darkgray,yellow,red),space=Lab),at=c(-6.01,6.01,51)) # or just using the colors you posted

Re: [R] Heatmap/Color Selection(Key)

sorry, typo: heatmap.2(x,col=colorRampPalette(c(blue,lightblue,darkgray,darkgray,yellow,red),space=Lab),at=c(-6.01,6.01,51)) heatmap.2(x,col=c(blue,lightblue,darkgray,black,darkgray,yellow,red),at=-3:3*2) should be read as

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