Error Bars In Ggplot
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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 To make graphs with
Ggplot Error Bar Width
ggplot2, the data must be in a data frame, and in “long” ggplot2 error bars (as opposed to wide) format. If your data needs to be restructured, see this page for more information. Sample r calculate standard error data The examples below will the ToothGrowth dataset. Note that dose is a numeric column here; in some situations it may be useful to convert it to a factor. class="n">tgGgplot Confidence Interval
Ggplot2 Stat_summary
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 1.799343 #> 6 VC 2.0 10 26.14 4.797731 1.5171757 3.432090 Line graphs After the data is summarized, we can make the graph. These are basic line an
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Error Bars In R
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geomgeom_abline geom_blank geom_errorbar geom_errorbarh geom_hline geom_jitter geom_linerange geom_point geom_pointrange geom_polygon geom_rect geom_rug geom_segment geom_step geom_text geom_vline position scale stat theme Recent http://sape.inf.usi.ch/quick-reference/ggplot2/geom_errorbar posts User login Username: * Password: * Request new password Home › Service › ggplot2 Quick Ref › geom ggplot2 Quick Reference: geom_errorbar A geom that https://egret.psychol.cam.ac.uk/statistics/R/graphs2.html draws error bars, defined by an upper and lower value. This is useful e.g., to draw confidence intervals. An error bar is similar to a pointrange error bar (minus the point, plus the whisker). It is also similar to a linerange (plus the whiskers). Default statistic: stat_identity Default position adjustment: position_identity Parameters x - (required) x coordinate of the bar ymin - (required) y coordinate of the lower whisker ymax - (required) y coordinate of the upper whisker size - (default: error bars in 0.5) thickness of the lines linetype - (default: 1=solid) the type of the lines colour - (default: "black") the color of the lines width - (default: 0.9) width of the whiskers alpha - (default: 1=opaque) the transparency of the lines Example This plot consists of two layers. The bottom layer shows error bars, and the top layer shows points. Note that we have to provide (or compute) the ymin and ymax values for the error bars ourselves (the errorbar geom does not automatically compute a confidence interval). d=data.frame(drink=c("coffee","tea","water"), mean=c(3,6,2), lower=c(2.6,5.6,1.8), upper=c(3.5,6.3,2.8)) ggplot() + geom_errorbar(data=d, mapping=aes(x=drink, ymin=upper, ymax=lower), width=0.2, size=1, color="blue") + geom_point(data=d, mapping=aes(x=drink, y=mean), size=4, shape=21, fill="white") + opts(title="geom_errorbar", plot.title=theme_text(size=40, vjust=1.5)) copyright (c) 2015 - sape research group Publication Highlights OOPSLA'15 - Use at Own Risk PPPJ'13 - Jikes RVM Debugger PLDI'12 - Algorithmic Profiling OOPSLA'11 - Catch Me ECOOP'11 - Beauty and Beast PLDI'10 - Profiler (In)Accuracy ASPLOS'09 - Measurement Bias More... Blast Our f
error bars Saving a graph to PDF, or PNG, or... Graph with free-floating SED bar Bar graph with error bars Another bar graph, with annotations Graph with multiple axis breaks Two-panel plot with horizontal and vertical error bars Prerequisite The ggplot2 library: library(ggplot2) If that doesn’t work, use install.packages("ggplot2") to install it, then retry. Not quite a prerequisite: add the ability to have left/bottom (without top/right) axes It’s hard to get ggplot to draw left and bottom axes only. Some use a post-processing hack (see http://wilke.openwetware.org/Creating_figures.html). I tried switching off all borders, using opts(panel.border = theme_blank()) and then using geom_hline(y=0) and geom_hline(y=0) to draw axes, which is OK, but it’s hard to get them positioned correctly. However, ggplot2 is open-source. So we can explore it: sudo apt-get install git to get the appropriate source code tools, then git clone https://github.com/hadley/ggplot2.git to fetch the source. And looking in theme-elements.r we can see the sort of thing to aim for. So we can create some code snippets which we can include in one line from rnc_ggplot2_border_themes_2011_03_17.r or rnc_ggplot2_border_themes_2013_01.r, like so: # For versions of ggplot2 around 0.8.7 / prior to Jan 2013: source("http://egret.psychol.cam.ac.uk/statistics/R/extensions/rnc_ggplot2_border_themes_2011_03_17.r") # For ggplot2 version 0.9.3 / from Jan 2013 onwards: source("http://egret.psychol.cam.ac.uk/statistics/R/extensions/rnc_ggplot2_border_themes_2013_01.r") This provides a number of possibilities but the theme_border() version is probably the easier to use. Its use is illustrated below: see opts( panel.border = theme_border(...) ). Data files used in these examples These files are all comma-separated value (CSV) text files: PhD_fig21A.csv PhD_fig37B.csv PhD_fig22D.csv PhD_fig23.csv PhD_fig28C.csv MD_fig30A.csv MD_fig30B.csv Let’s load them all in, to begin with: phdfig37b = read.table("PhD_fig37B.csv", header=TRUE, sep=",", na.strings="NA", dec=".", strip.white=TRUE) phdfig21a = read.tab