similar to: Enhanced heatmap, barplot functions

To all, Recently I created a version of barplot() to include some new features as follows: 1. Plot confidence intervals for each bar: The user can pass lower (ci.l) and upper (ci.u) bounds in the same vector/matrix format as "height". The CI boundary lines will vary in width per bar, if a varying "width" argument is specified. CI line width, type and color can be

Version 0.6.0 of the gregmisc package has just been released on CRAN. Description: =========== Package: gregmisc Description: Misc Functions written/maintained by Gregory R. Warnes Title: Greg's Miscellaneous Functions Version: 0.6.0 Date: 2002/09/23 Maintainer: Gregory R. Warnes <Gregory_R_Warnes at groton.pfizer.com> Author: Gregory R. Warnes. Includes code provided by Ben

Version 0.6.0 of the gregmisc package has just been released on CRAN. Description: =========== Package: gregmisc Description: Misc Functions written/maintained by Gregory R. Warnes Title: Greg's Miscellaneous Functions Version: 0.6.0 Date: 2002/09/23 Maintainer: Gregory R. Warnes <Gregory_R_Warnes at groton.pfizer.com> Author: Gregory R. Warnes. Includes code provided by Ben

Dear R Users, (and dear Marc) First of all many thanks for the answers to my previous questions. I would like to barplot the mean percent change of a variate with it's CI. Bars should start from the zero reference line to height (in barplot2). Is there a way to tweak barplot2, for example, to do that ? I have tried to see what the function was but unlike other functions was not able to

Hi,   I need to generate a heatmap on a square matrix and wouldn't want to reorder the columns and the rows on the heatmap display.    I have used the options Rowv=NULL and Colv=NULL but doesn't seem to work. Following is a snippet of the heatmap function i am using. args <- commandArgs(); inputfile <- args[2] imgfile   <- args[3] bitmap(imgfile, height=15, width=15, res=100,

Version 0.8.0 of the gregmisc package is now (or will shortly be) available on CRAN. New in this release: - Enhanced and bug-fixed 'CrossTable' function (contributed by Marc Schwartz) - Augmented the 'barplot2' function with an 'add' argument to allow for the addition of a barplot to an existing graphic. (contributed by Marc Schwartz) - Added the

R-Users, Hopefully someone can shed some light on these questions as I had little luck searching the archives (although I probably missed something in my search due to the search phrase). I estimated multinomial probabilities for some count data (number successful offspring) ranging from 0 to 8 (9 possible response categories). I constructed a barplot (using barplot2) and I want to

This in an enhancement requestion, to add the capability to pass arguments through barplot() to legend(). I've created a version that does this. # Run this code; notice that the legend # is superposed over one bar: barplot(height = cbind(x = c(465,91) / 465 * 100, y = c(840,200) / 840 * 100, z = c(37,17) / 37 * 100), beside = FALSE, width =

When I use the image() function for a relatively small matrix it works perfectly, eg.x <- 1:100 > z <- matrix(rnorm(10^4),10^2,10^2) > image(x=x,y=x,z=z,col=rainbow(3))but when I want to plot a larger matrix, it doesn't really work. Most of the times, it just plot a few intermitent points.x <- 1:1000 z <- matrix(rnorm(10^6),10^3,10^3) image(x=x,y=x,z=z,col=rainbow(3))

Full_Name: Elizabeth Purdom Version: 1.9.1 OS: Windows XP Submission from: (NULL) (171.64.102.199) It would be great if heatmap and/or image had the option of printing a legend bar on it somewhere that would indicate the ranges given by the colors in the heatmap (i.e. a very small image rectangle with the same colors as in the heatmap). Because heatmap is using layout, it seems pretty

Hello does anyone know what algorithm is used to produce the hierarchical clustering in the gplots package using the function heatmap.2? I think it may be the complete linkage clustering algorithm, but I can't find a source that seems reliable. Thank you and sorry if I posted this in the wrong place. If I have, please let me know and I will move it to the appropriate list. -- View this

Hi, I have trouble with the heatmap function (package stats). The row labels are wrongly ordered and don't correspond to the Rowv dendrogram. I know there is a bug with the heatmap fonction. Emmanuel Paradis (http://tolstoy.newcastle.edu.au/R/e2/help/07/05/16227.html )suggested a modification to fix it but in my case the row labels are still wrongly ordered. Heatmaps with 2 phylograms have

I am using barplot, and barplot2 in the gregmisc bundle, in the following way: barplot2(sort(xtabs(expend / 1000 ~ theme)), col = c(mdg7, mdg8, mdg3, mdg1), horiz = T, las = 1, xlab = "$ '000", plot.grid = T) The problem is that the values of 'theme', which is a factor, are in some cases rather long, so that I would like to wrap/split them at a space once they

I want to include missing values in my barplot to get the correct x-axis, for example, x <- c(1,2,3,4, 9) y <- c(2,4,6,8,18) barplot(y) The above looks wrong because the last height in y should be a long way over. So I want to do something like... x <- c(1,2,3,4,5,6,7,8, 9) y <- c(2,4,6,8,0,0,0,0,18) barplot(y) However... I am actually using barplot2 to use the

Hello, I try to handle a simple bar-plot, but it turns out to be not as simple as I thought. 1) I have created a .dat-File, e.g. test.dat: DATA DATA-SEM 2.2 0.32 6.2 1.30 12.7 1.61 48.6 3.08 4.1 0.86 4.5 0.32 1.5 1.13 1.2 1.08 The first row is the data represented by bars. The second row deals with the Standard Error of Mean. The lines correspond to time-intervals of experiments. 2) I now

On 1/27/2017 8:30 AM, danielrenato at lycos.com wrote: > Hello developers folks! > > First, congratulations for the wonderful work with R. > > For science, barplots with error bars are very important. We were > wondering that is so easy to use the boxplot function: > > boxplot(Spores~treatment, col=treatment_colors) > > But there is no such function for barplots with

I need to increase the width of the border in a barplot, i checked both barplot, and barplot2, but cant find how to do it. how can I do? thank you john [[alternative HTML version deleted]]

I would like to preface this by saying that I have not been using R for long, and consider myself a beginner. But the more I use and learn R, the more impressed I am with both the 'product' itself, and the efforts of those developing it. It has been noted (eg Duncan Murdoch, 15 April), that the barplot function in R 1.9.0, when used on a tabulated single factor, produces a plot only one

I have a barplot I have created using barplot2 and I have been able to add points and lines (using the points and lines methods, respectively). I now need to add some polygons (triangles in particular), that I want to be shaded to match bars in the plot. I can get the coordinates of the corners of the triangles, but don't know how to draw the triangles. I know there is the grid.polygon

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate