search for: volcano

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 <- 10*(1:ncol(volcano)) image(x, y, volcano, col = terrain.colors(100), axes = FALSE) contour(x, y, volcano, levels...

hi dear R crew. may i request the script for volcano plot. if able, pls include any tips about volcano plot. thank you. [[alternative HTML version deleted]]

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 command: filled.contour(x,y,volcano, plot.axes={axis(...

...ot? 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 <- 10*(1:ncol(volcano)) image(x, y, volcano,col = terrain.colors(100),axes = FALSE) contour(x, y, volcano, levels = seq(90, 200, by=5),add = TRUE, col = "peru") axis(1, at = seq(100, 800, by = 100)) axis(2, at = seq(100, 600, by = 100)) box() title(main...

...--- 1,6 ---- ###-*- R -*- ! ! opar <- par(ask = interactive() && .Device == "X11") # For source # Here is some code which illustrates some of the differences between # R and S graphics capabilities. Note that colors are generally specified *************** data("volcano") *** 115,121 **** x <- 10*1:nrow(volcano) y <- 10*1:ncol(volcano) l <- pretty(range(volcano), 10) ! opar <- par(bg="lightcyan") pin <- par("pin") xdelta <- diff(range(x)) ydelta <- diff(range(y)) --- 116,122 ---- x <- 10*1:nrow(volcano...

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) ## 2nd plot op <- squishplot(range(x),range(y),1) image(x, y, volcano, col = terrain.colors(100)...

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]]

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]]

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") +...

Dear R-Help community, I am trying to overlay a single contour line over a correlation plot using levelplot in the lattice package. These are the two arrays: 1) a correlation plot over Africa - so each grid square is a different colour dependent on correlation - this is in an array: result_cor with dim[465,465] 2) a single contour line from a ***different data source*** - this is from data

Karline, Thank you for your help. I discovered that in addition to including clim, I needed to omit breaks. This code uses one of your other examples as a starting point and works as intended: persp3D(z = volcano, zlim = c(-60, 200), phi = 20, colkey = list(length = 0.2, width = 0.4, shift = 0.15, cex.axis = 0.8, cex.clab = 0.85), lighting = TRUE, lphi = 90, clab = c("","height","m"), bty = "f", plot = FALSE) elev.classes <- matrix(findInter...

...xs = xaxs, This provides all the support of axis.POSIXt that plot.default gives, currently the default new plot in image.default uses NAs and the axis class is ignored. This is nice for plotting time series data stored in a matrix. Here's a dummy example that shows usage with my change: data(volcano) x <- list(x = Sys.time() + seq(1, 1e6, length = nrow(volcano)), y = 1:ncol(volcano), z = volcano) ## date-time formatting on the x-axis image(x) ## date-time formatting on the y-axis image(x$y, x$x, t(x$z)) Without the change we get the very large underlying numeric values for the times on t...

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 = seq(1:10), axes = FALSE) # O puedes usar su nombre colors()[1:5] image(x, y, volcano, col = colors()[401:500], axes =...

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...

Hi, I have a matrix of data which i can vizualize as an image - for example. I would like to save this image as a geotiff file or at a tiff file with a world file which holds the projection of my data (ultimately the data represent a map of some sort). I know i can save the data as an ESRI grid, but i am not interested in that. I wonder if anybody knows about any code which will help me do

Hello all, I was trying to make a volcano plot with some real data, using log2(ratio) vs. Z-value significance. However the scatter of the points is too less contrary to 'normal' volcano plots and I'm getting a sharp 'V' shaped plot. *Am I doing something wrong here?* The data(ratio) is available from pastebin: htt...

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=...

I am using the lattice packge for its levelplot and contourplot. Is it possible to adjust the line thickness of the 'box' and tickmarks in these plots? Thanks for the attention, Matt Sundling

...I want is to make a image plot look nicer. with image() it looks very facetted, and I would like to make it look smoother. I've tried with interp.surface() in fields package but it (obviously) makes nan values at the borders and around nan. Maybe an example would make me explain better: data(volcano) par(mfrow=c(1,2)) x <- 10*(1:nrow(volcano)) y <- 10*(1:ncol(volcano)) volcano[seq(1,87,by=10),seq(1,61,by=10)]<-NA; image(x, y, volcano, col = terrain.colors(100)) ## This is what I've tried with interp.surface() library(fields) newx<-seq(10,870,by=2); newy<-seq(10,610,by=2); vo...

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)? Apo...