Graphing Error Bars R
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Error Bar In R
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programmers, just like you, helping each other. Join them; it only takes a minute: Sign up Scatter plot with error bars up vote 21 down vote favorite 11 How can I generate the following plot in https://www.r-bloggers.com/building-barplots-with-error-bars/ R? Points, shown in the plot are the averages, and their ranges correspond to minimal and maximal values. I have data in two files (below is an example). x y 1 0.8773 1 0.8722 1 0.8816 1 0.8834 1 0.8759 1 0.8890 1 0.8727 2 0.9047 2 0.9062 2 0.8998 2 0.9044 2 0.8960 .. ... r plot share|improve this question edited Oct 23 '12 at 15:10 Roland 73.5k463102 asked Oct 23 '12 http://stackoverflow.com/questions/13032777/scatter-plot-with-error-bars at 14:29 sherlock85 1521313 Since you clearly don't want a boxplot, I changed the title of your question in order to reflect what you really want. –Roland Oct 23 '12 at 15:11 1 also plotrix::plotCI, gplots::plotCI, library("sos"); findFn("{error bar}") –Ben Bolker Oct 23 '12 at 17:29 add a comment| 5 Answers 5 active oldest votes up vote 52 down vote accepted First of all: it is very unfortunate and surprising that R cannot draw error bars "out of the box". Here is my favourite workaround, the advantage is that you do not need any extra packages. The trick is to draw arrows (!) but with little horizontal bars instead of arrowheads (!!!). This not-so-straightforward idea comes from the R Wiki Tips and is reproduced here as a worked-out example. Let's assume you have a vector of "average values" avg and another vector of "standard deviations" sdev, they are of the same length n. Let's make the abscissa just the number of these "measurements", so x <- 1:n. Using these, here come the plotting commands: plot(x, avg, ylim=range(c(avg-sdev, avg+sdev)), pch=19, xlab="Measurements", ylab="Mean +/- SD", main="Scatter plot with std.dev error bars" ) # hack: we draw arrows but with very special "arrowheads" arrows(x, avg-sdev, x, avg+sdev, length=0.05, angle=90, code=3) The result looks like this: In the ar
Diet & Nutrition (28) Education (1) Evolution (35) Human Ecology (75) Infectious Disease (66) LaTeX (5) Primates (9) R (12) science (17) Social Network Analysis (17) Statistics (16) Teaching (10) Uncategorized (28) Meta Log in http://monkeysuncle.stanford.edu/?p=485 Entries RSS Comments RSS WordPress.org ← Latest Swine Flu Epidemic Curve for the http://moderndata.plot.ly/easy-error-bars-with-r-and-plotly/ United States Stanford Workshop in Biodemography → Plotting Error Bars in R August 24th, 2009 · 52 Comments · R One common frustration that I have heard expressed about R is that there is no automatic way to plot error bars (whiskers really) on bar plots. I just encountered this issue revising a error bar paper for submission and figured I'd share my code. The following simple function will plot reasonable error bars on a bar plot. PLAIN TEXT R: error.bar <- function(x, y, upper, lower=upper, length=0.1,...){ if(length(x) != length(y) | length(y) !=length(lower) | length(lower) != length(upper)) stop("vectors must be same length") arrows(x,y+upper, x, y-lower, angle=90, code=3, length=length, ...) } Now let's use it. First, I'll create 5 means drawn from error bars r a Gaussian random variable with unit mean and variance. I want to point out another mild annoyance with the way that R handles bar plots, and how to fix it. By default, barplot() suppresses the X-axis. Not sure why. If you want the axis to show up with the same line style as the Y-axis, include the argument axis.lty=1, as below. By creating an object to hold your bar plot, you capture the midpoints of the bars along the abscissa that can later be used to plot the error bars. PLAIN TEXT R: y <- rnorm(500, mean=1) y <- matrix(y,100,5) y.means <- apply(y,2,mean) y.sd <- apply(y,2,sd) barx <- barplot(y.means, names.arg=1:5,ylim=c(0,1.5), col="blue", axis.lty=1, xlab="Replicates", ylab="Value (arbitrary units)") error.bar(barx,y.means, 1.96*y.sd/10) Now let's say we want to create the very common plot in reporting the results of scientific experiments: adjacent bars representing the treatment and the control with 95% confidence intervals on the estimates of the means. The trick here is to create a 2 x n matrix of your bar values, where each row holds the values to be compared (e.g., treatment vs. control, male vs. female, etc.). Let's look at our same Gaussian means but now compa
dataset, and are easy to graph with Plotly and R! Error bars can be used to visualize standard deviations, standard errors or confidence intervals (just don't forget to specify which measure the error bar in the graph represents). Below are two examples that demonstrate how to graph a variety of error bars. The complete R script and data used to create these 2 graphs are available here! To create vertical error bars, like on the Snow line in the graph below, set error_y = list(type = "data", array = c(YOUR_VALUES)) 1 error_y = list(type = "data", array = c(YOUR_VALUES))
It is also possible to calculate and plot error bars with a percent value, like on the Rain line below. Set: error_y = list(type = "percent", value = CHOOSE_%_VALUE) 1 error_y = list(type = "percent", value = CHOOSE_%_VALUE) To create horizontal error bars use error_x. Furthermore, it's easy to graph asymmetrical error bars. Just set symmetric = FALSE and add an arrayminus array like this: error_x = list( type = "data", symmetric = FALSE, array = c(YOUR_HIGH_VALUES), arrayminus = c(YOUR_LOW_VALUES)) 12345 error_x = list(type = "data",symmetric = FALSE,array = c(YOUR_HIGH_VALUES),arrayminus = c(YOUR_LOW_VALUES)) Creating dashboards or visualizations at your company? Consider Plotly Enterprise for modern intracompany graph and data sharing. chelsea Tags: confidence interval, Error bars, Plotly, R, RStudio, standard deviation, standard error Post navigation Previous Post 3d surface plots with RStudio and PlotlyNext Post Using R, Python, & Plotly With Tableau Search for: Search Recent Posts Visualizing ROC Curves in R using Plotly nteract: Revolutionizing the Notebook Experience Simple REST APIs for charts and datasets Upgrading to plotly 4.0 (and above) Radial Stacked Area Chart in R using Plotly R Visualizing ROC Curves in R using Plotly Upgrading to plotly 4.0 (and above) Radial Stacked Area Chart in R using Plotly Using cranlogs in R with Plotly New feature: Dropdown menus in Plotly and R Blog roll R-Bloggers