similar to: highlighting clusters in a heatmap

Hi, I'm trying to build dendrograms to pass to heatmap(). The dendrograms I build plot properly, but when I pass them to heatmap() I get the error message "row dendrogram ordering gave index of wrong length" (see output log below). I looked in the code of heatmap() and saw that the error was due to a NULL return value from order.dendrogram(), which in turn got a NULL return value

Hi, I am using the function heatmap(stats) to draw a microarray heatmap, columns are samples and rows are gene features. I did a 2D clustering during the heatmap drawing. The features and samples indeed cluster into several blocks both vertically and horizontally. I can get the index of re-ordered rows and columns after the heatmap drawing by typing the the return variable of the heatmap

Hi R fans, As a newbie following the five-hour rule (after hitting my head against the wall for five hours, post to this list), I am appealing for some help understanding geom_rect() in ggplot2. What I want to do is very simple. I want to generate a plot of rectangles. Each one represents a business cycle. The x-values will be pairs representing the start and end of each cycle. The y-values

plot.hclust: Setting up a window for a dendrogram assumes the first link is the shortest and the last is the longest. This is not always the case when the clustering was done with hclust, method="median" or method="centroid", and the dendrogram sometimes doesn't fit within the window. I propose the fix listed below. src/main/ --- plot.c Wed Sep 17 01:03:39 2003 +++

Dear R-ers, I hope there is a really simple solution to my problem. I've written a function that I saved in an .r file. I source this file in my code. For a while it worked fine. But then when I run the line: source("F mylineplot.r") I started getting a warning: In readLines(file) : incomplete final line found on 'F mylineplot.r' I have no idea why - I tried to check and

I have a xml exported by Manifold GIS but I'm not being able to import it into R using XLM package. The file have this structure: <?xml version="1.0" encoding="UTF-8" ?> - <layout> <name>Layout 2</name> <pagesByX>1</pagesByX> <pagesByY>1</pagesByY> - <elements> <legend

Hello I have created a graph using the following commands: <<< startBReP3O1T <- diffs$BReP3O1T - diffs$diff_BReP3O1T endBReP3O1T <- diffs$BReP3O1T x <- seq(47,89, length = 10) ymin <- min(min(startBReP3O1T), min(endBReP3O1T)) ymax <- max(max(startBReP3O1T), max(endBReP3O1T)) y <- seq(ymin, ymax, length = 10) plot(x,y, type = 'n', xlab = 'Age', ylab =

Hello All: Can anybody tell me what is the problem with my program please. I have an error message as appears below. My program is: ifn <- "Jul08_09.LM" data <- read.table(ifn) ofn <- "Jul.png" bitmap(ofn, type = "png256", width = 30, height = 30, pointsize = 30, bg = "white",res=50) par(mar=c(5, 5, 3, 2),lwd=5)

Dear All, I have this script: dat <- data.frame(Month = hstat$Date,C_avg = hstat$C.avg,C_stdev = hstat$C.stdev) ggplot(data = dat, aes(x = Month, y = C_avg, ymin = C_avg - C_stdev, ymax = C_avg + C_stdev)) + geom_point() + geom_line() + geom_errorbar() dat <- data.frame(Month = hstat$Date,K_avg = hstat$K.avg,K_stdev = hstat$K.stdev) ggplot(data = dat, aes(x = Month, y = K_avg,

Dear List, I am having trouble setting the transparency of a ribbon in ggplot2 and was wondering if anybody had any suggestions so far i have a plot exactly as i want it and i want to add a ribbon connecting the ymax and ymin, whci i do with the following command m10 + stat_summary(geom="ribbon", fun.ymin="min", fun.ymax="max") However the ribbon is a dark grey

Hello, I am trying to add a less than equal to symbol in a ggplot2 legend text. See sample code below. I have tried using the expression function and \u2264. I also tried adding labels to legend.text under theme. Neither of these 3 options work. Please help, Mahesh ++++++++++++++ Extra.column=ifelse(data[,covariate]>cutpoint,1,0) Grp1 <- "\u2264 1.5" Grp2 <-

Hi, I would like to plot a bunch of tree ring width data (time series) using ggplots, but I'm having trouble figuring out how to do it. My data is in a data.frame, with years as rownames and a distinct tree ring series in each column. So, something like this: rwl<-matrix(rnorm(800), nrow = 100) colnames(rwl) <- paste('V', 1:8, sep = '')

Hello, I'm attempting to plot error bars side by side rather than stacked on top of each other with ggplot2. Here is the sample code I am using: #Code #Data spd<-c("s","f","f","s","f","s","s","s","f","f","s","f") r<-c(4.9,3.2,2.1,.2,3.8,6.4,7.5,1.7,3.4,4.1,2.2,5)

Hi Put fill outside aes p+geom_ribbon(aes(ymin = slope_1*x + intercept_1 - 1/w[2], ymax = slope_1*x + intercept_1 + 1/w[2]), fill = "blue", alpha=0.1) The "hole" is because you have two levels of data (red and blue). To get rid of this you should put new data in ribbon call. Something like newdat <- trainset newdat$z <- factor(0) p+geom_ribbon(data=newdat, aes(ymin =

Hola a tod en s, bueno, un poco al hilo de un mensaje anterior, reformulo la pregunta y pongo código completamente reproducible, a ver si hay más suerte. Estoy con un informe y hay que hacer algunos gráficos con datos diferentes con ggplot2, y hay que poner el mismo tamaño para todos ellos. El problema es que R cambia automáticamente el tamaño del área de trazado y el margen en función de

G'day Thomas, On Sat, 12 Aug 2023 04:17:42 +0000 (UTC) Thomas Subia via R-help <r-help at r-project.org> wrote: > Here is my reproducible code for a graph using geom_smooth The call "library(tidyverse)" was missing. :) > I'd like to add a black boundary around the shaded area. I suspect > this can be done with geom_ribbon but I cannot figure this out. Some >

Consider the following situation: we have quantified algal concentrations for a variety of species using many samples at each of three years. It seems to make sense to generate a line plot (matplot-like), with each species plotted as a separate line, with the points connected to emphasize the temporal pattern. The problem: lots of overlapping error bars. The question: from both a

?s 05:17 de 12/08/2023, Thomas Subia via R-help escreveu: > Colleagues, > > Here is my reproducible code for a graph using geom_smooth > set.seed(55) > scatter_data <- tibble(x_var = runif(100, min = 0, max = 25) > ?????????????????????? ,y_var = log2(x_var) + rnorm(100)) > > library(ggplot2) > library(cowplot) > > ggplot(scatter_data,aes(x=x_var,y=y_var))+

I've wrote some code to simulate a random walk in 2 dimensions on a lattice. Basically I want to add something in to make it plot it point by point so you can see what is going on. Heres my code for the random walk in 2d RW2D<-function(N) { i<-0 xdir<-0 ydir<-0 xpos<-vector() xpos[1]<-xdir ypos<-vector() ypos[1]<-ydir for (i in 1:N-1)

Buenas, una pregunta. Si yo estoy calculando un modelo lineal, el caso más simple, 1 variable respuesta y una variable explicativa y creo un modelo, me da un R2 del 80% y quiero ver como es esa relacion entre las variables, para calcular el error de predicción del modelo, basta con ver el intervalo de confianza del modelo e irme a los extremos? Por si no me he expresado bien, un ejemplo tonto: