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HELLO, anybody... could you help me to check the below coding for volcano. what is the mistake? what the plot could not display? # volcano_plot.r # # Author: Amsha Nahid, Jairus Bowne, Gerard Murray # Purpose: Produces a volcano plot # # Input: Data matrix as specified in Data-matrix-format.pdf # Output: Plots log2(fold change) vs log10(t-test P-value) # #

Hello. My name is Akashah. i work at metabolic laboratory. From my study, i found that volcano plot can help a lot in my section.  i already studied about the volcano plot and get the coding to run in R software, unfortunately, there is may be something wrong with the coding. This is because  no graph appear, but no error (blue color text) was shown on the R console. Below is the coding for

Error in lda.default(x, grouping, ...) : variables 1 3 5 8 10 15 17 20 27 29 34 appear to be constant within groups what this sentence means?? [[alternative HTML version deleted]]

Dear All, I was looking for the color index in?image function,?such as from topo.colors(n) and etc. but still never found it. For instance, from the help menu. ########################################### # Volcano data visualized as matrix. Need to transpose and flip # matrix horizontally. image(t(volcano)[ncol(volcano):1,]) # A prettier display of the volcano x <- 10*(1:nrow(volcano)) y

Do you know what steps I need to take to add a scale to a plot? I'm pulling my example out of "An Introduction to R: Software for StatisticalModelling & Computing" (see the R code around Figure 76). I would like to add a scale to the image produced by the following code.? I would like to the scale to list the distance?and units:? data(volcano) x <- 10*(1:nrow(volcano)) y

Dear all, I am using filled.contour and my x-axis consists of a vector of dates, formatted using as.POSIXct. When I assign this vector to x in filled.contour, the x-axis in the plot is correctly formatted as dates. However, when I use plot.axes=axis(1) in filled.contour the x-axis is not correctly formatted. I need to opt for the latter because I want to add additional lines and points to the

Dear all, I would like to generate a filled.contour plot with log x and y axis, however using: filled.contour(as.line,log="xy") results in a warning message. Does anybody knos what to do? Thanks Thomas

hello, i'm searching the r-coding to plot wilcoxon signed test. i already searched everywhere for a month, but i didn't found it. Could anyone help me, please. [[alternative HTML version deleted]]

can you recommend a good manual for R that starts with a data set and gives demonstrations on what can be done using R? I downloadedR Langauage definition and An introduction to R but haven't found them overly useful. I'd really like to be able to follow some tutorials using a dataset or many datasets. The datasets I have available on R are Data sets in package 'datasets':

Hi R-help community, Can anyone tell me why, while using : x <- seq(as.Date("2001-01-01"),as.Date("2001-01-01") + nrow(volcano)-1,1) y <- seq(1, ncol(volcano),1) when I plot the volcano matrix with that command : filled.contour(x,y,volcano) the graph has a Date format on X-axis, ok ... ... but when adding a contour plot to the filled contour, using this

Hi list, I wonder if anyone has had this experience with squishplot() in the TeachingDemos package. Taking the example from the ?image help page, library(TeachingDemos) x <- 10*(1:nrow(volcano)) y <- 10*(1:ncol(volcano)) layout(matrix(c(1,2,3,4),ncol=2,byrow=TRUE),height=c(2,1)) ## 1st plot op <- squishplot(range(x),range(y),1) image(x, y, volcano, col = terrain.colors(100)) par(op)

Hi! Whenever I save a graphic in ps/eps format generated by filled.contour or image, an undesired grid is added to it (not visible on the X11 screen). For example: postscript("volcano.eps") filled.contour(volcano,col=gray(seq(0,1,,50)),levels=seq(min(volcano),max(volcano),,50)) dev.off() Any ideia how to eliminate this grid? Thanks, Rachel [[alternative HTML version deleted]]

Hello, I would like to suggest the following change to image.default in src\library\graphics\R\image.R: 98c98 < plot(NA, NA, xlim = xlim, ylim = ylim, type = "n", xaxs = xaxs, --- > plot(x[1], y[1], xlim = xlim, ylim = ylim, type = "n", xaxs = xaxs, This provides all the support of axis.POSIXt that plot.default gives, currently the default new plot in

Como usas la función image puedes consultar la ayuda ?image o help(image) y encontrarás el siguiente ejemplo donde se usa un diferente color Palette (mencionada por pepeceb en su respuesta). x <- 10*(1:nrow(volcano)) y <- 10*(1:ncol(volcano)) image(x, y, volcano, col = terrain.colors(100), axes = FALSE) # O puedes usar directamente el número para indicar el color image(x, y, volcano, col =

Given the example: R> (levs <- quantile(volcano,c(0,0.1,0.5,0.9,0.99,1))) 0% 10% 50% 90% 99% 100% 94 100 124 170 189 195 R> levelplot(volcano,at=levs) How can I make the key categorical with the size of the divisions equally spaced in the key? E.g., five equal size rectangles with labels at levs c(100,124,170,189,195)? Apologies if this is obvious. -A R> version

Quick question - I am having problems creating an orographic image (similar to volcano example). I have created a map matrix with 3 columns and over 2million rows. I have created the matrix as follows: map<-read.table("map.dat",header=TRUE) long.grid<-sort(unique(map$long) lat.grid<-sort(unique(map$lat) map.matrix<-matrix(map$height,nrow=length(lat.grid),byrow=TRUE) The

Dear R gurus, I have got stuck on how to customise the colorkey generated by levelplot and contourplot, in the lattice package. This best illustrated by an example: library(lattice) levelplot(volcano^20/1e45,at=c(0,0.001,0.01,0.1,1,10)) The reason for raising the volcano dataset to the 20th power is to create a dataset with a large vertical exaggeration - this is similar in nature to the data

Hi I am using the ggplot2 package for the volcano plot and I am using the following code for the same: g = ggplot(data=data, aes(x=data[11], y=-log10(data[12]), colour=threshold)) + + geom_point(alpha=0.4, size=1.75) + + opts(legend.position = "none") + + xlim(c(-10, 10)) + ylim(c(0, 15)) + + xlab("log2 fold change") + ylab("-log10 p-value") data[11] is a

The line contour(volcano, x, y, l, col = "yellow", lty = "solid", add = TRUE) needs to be changed to contour(x, y, volcano, col = "yellow", lty = "solid", add = TRUE) A patch is appended below. -k *** demos/graphics/graphics.orig Thu Apr 17 11:02:39 1997 --- demos/graphics/graphics Thu Apr 17 11:03:08 1997 *************** plot(numeric(0), numeric(0),

Can't installe packag maDB or limma. Error is shown as Using R version 2.13.1, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages: Is there any other way to draw volcano plot ? Thanks [[alternative HTML version deleted]]