Plot With Error Bars R
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Scatter Plot With Error Bars In R
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Errbar R
down vote favorite 11 How can I generate the following plot in 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 .. ...
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r plot share|improve this question edited Oct 23 '12 at 15:10 Roland 74.1k463103 asked Oct 23 '12 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="Measure
error bars Two within-subjects variables Note about normed means Helper functions Problem You want to plot means and error bars for a dataset. Solution r arrows To make graphs with ggplot2, the data must be in a
Ggplot2 Error Bars
data frame, and in “long” (as opposed to wide) format. If your data needs to be restructured, plot mean and standard deviation in r see this page for more information. Sample data The examples below will the ToothGrowth dataset. Note that dose is a numeric column here; in some situations it may http://stackoverflow.com/questions/13032777/scatter-plot-with-error-bars be useful to convert it to a factor. tg <- ToothGrowth head(tg) #> len supp dose #> 1 4.2 VC 0.5 #> 2 11.5 VC 0.5 #> 3 7.3 VC 0.5 #> 4 5.8 VC 0.5 #> 5 6.4 VC 0.5 #> 6 10.0 VC http://cookbook-r.com/Graphs/Plotting_means_and_error_bars_(ggplot2)/ 0.5 library(ggplot2) First, it is necessary to summarize the data. This can be done in a number of ways, as described on this page. In this case, we’ll use the summarySE() function defined on that page, and also at the bottom of this page. (The code for the summarySE function must be entered before it is called here). # summarySE provides the standard deviation, standard error of the mean, and a (default 95%) confidence interval tgc <- summarySE(tg, measurevar="len", groupvars=c("supp","dose")) tgc #> supp dose N len sd se ci #> 1 OJ 0.5 10 13.23 4.459709 1.4102837 3.190283 #> 2 OJ 1.0 10 22.70 3.910953 1.2367520 2.797727 #> 3 OJ 2.0 10 26.06 2.655058 0.8396031 1.899314 #> 4 VC 0.5 10 7.98 2.746634 0.8685620 1.964824 #> 5 VC 1.0 10 16.77 2.515309 0.7954104 1.799
|| is.character(x)) "" else as.character(substitute(y)), add=FALSE, lty=1, type='p', ylim=NULL, lwd=1, pch=16, Type=rep(1, length(y)), ...) Arguments x vector of numeric x-axis values (for vertical error bars) or a factor or character variable (for horizontal error bars, x representing the group labels) y vector of http://svitsrv25.epfl.ch/R-doc/library/Hmisc/html/errbar.html y-axis values. yplus vector of y-axis values: the tops of the error bars. yminus vector of y-axis values: the bottoms of the error bars. cap the width of the little lines at the tops and bottoms of the error bars in units of the width of the plot. Defaults to 0.015. main a main title for the plot, see also title. sub a sub title for the plot. xlab optional x-axis labels if add=FALSE. ylab error bars optional y-axis labels if add=FALSE. Defaults to blank for horizontal charts. add set to TRUE to add bars to an existing plot (available only for vertical error bars) lty type of line for error bars type type of point. Use type="b" to connect dots. ylim y-axis limits. Default is to use range of y, yminus, and yplus. For horizonal charts, ylim is really the x-axis range, excluding differences. lwd line width for line segments (not main line) plot with error pch character to use as the point. Type used for horizontal bars only. Is an integer vector with values 1 if corresponding values represent simple estimates, 2 if they represent differences. ... other parameters passed to all graphics functions. Details errbar adds vertical error bars to an existing plot or makes a new plot with error bars. It can also make a horizontal error bar plot that shows error bars for group differences as well as bars for groups. For the latter type of plot, the lower x-axis scale corresponds to group estimates and the upper scale corresponds to differences. The spacings of the two scales are identical but the scale for differences has its origin shifted so that zero may be included. If at least one of the confidence intervals includes zero, a vertical dotted reference line at zero is drawn. Author(s) Charles Geyer, University of Chicago. Modified by Frank Harrell, Vanderbilt University, to handle missing data, to add the parameters add and lty, and to implement horizontal charts with differences. Examples set.seed(1) x <- 1:10 y <- x + rnorm(10) delta <- runif(10) errbar( x, y, y + delta, y - delta ) # Show bootstrap nonparametric CLs for 3 group means and for # pairwise differences on same graph group <- sample(c('a','b','d'), 200, TRUE) y <- runif(200) + .25*(group=='b') + .5*(group=='d') cla <- smean.cl.boot(y[group=='a'],B=100,reps=TRUE) # usuall