Bar Chart R Error Bars
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eRum 2016 sponsors The Simpsons by the Data Other sites Jobs for R-users SAS blogs Building Barplots with Error Bars August 17, 2015By Chris Wetherill (This article was first published on DataScience+, and kindly contributed to R-bloggers) Bar charts are a pretty common way to represent data visually, but constructing them isn't always the most intuitive thing in the world. One way that we can construct these graphs is using R's default packages. Barplots using base R Let's start by viewing our dataframe: here we will be finding the mean miles per gallon by number of cylinders and number of gears. View(mtcars) We begin by aggregating our data by cylinders and gears and specify that we want to return the mean, standard deviation, and number of observations for each group: myData <- aggregate(mtcars$mpg, by = list(cyl = mtcars$cyl, gears = mtcars$gear), FUN = function(x) c(mean = mean(x), sd = sd(x), n = length(x))) After this, we'll need to do a little manipulation since the previous function returned matrices instead of vectors myData <- do.call(data.frame, myData) And now let's compute the standard error for each group. We can then rename the columns just for ease of use. myData$se <- myData$x.sd / sqrt(myData$x.n) colnames(myData) <- c("cyl", "gears", "mean", "sd", "n", "se") myData$names <- c(paste(myData$cyl, "cyl /", myData$gears, " gear")) Now we're in good shape to start constructing our p
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answers to any questions you might have Meta Discuss the workings and policies barplot with error bars matlab of this site About Us Learn more about Stack Overflow the company Business Learn more about hiring developers or posting https://www.r-bloggers.com/building-barplots-with-error-bars/ ads with us Stack Overflow Questions Jobs Documentation Tags Users Badges Ask Question x Dismiss Join the Stack Overflow Community Stack Overflow is a community of 4.7 million programmers, just like you, helping each other. Join them; it only takes a http://stackoverflow.com/questions/29768219/grouped-barplot-in-r-with-error-bars minute: Sign up Grouped barplot in R with error bars up vote 4 down vote favorite 1 Dear Stackoverflow users, I would like to draw a grouped barplot with error bars. Here is the kind of figure I have been able to get up to now, and this is ok for what I need: And here is my script: #create dataframe Gene<-c("Gene1","Gene2","Gene1","Gene2") count1<-c(12,14,16,34) count2<-c(4,7,9,23) count3<-c(36,22,54,12) count4<-c(12,24,35,23) Species<-c("A","A","B","B") df<-data.frame(Gene,count1,count2,count3,count4,Species) df mean1<-mean(as.numeric(df[1,][c(2,3,4,5)])) mean2<-mean(as.numeric(df[2,][c(2,3,4,5)])) mean3<-mean(as.numeric(df[3,][c(2,3,4,5)])) mean4<-mean(as.numeric(df[4,][c(2,3,4,5)])) Gene1SpeciesA.stdev<-sd(as.numeric(df[1,][c(2,3,4,5)])) Gene2SpeciesA.stdev<-sd(as.numeric(df[2,][c(2,3,4,5)])) Gene1SpeciesB.stdev<-sd(as.numeric(df[3,][c(2,3,4,5)])) Gene2SpeciesB.stdev<-sd(as.numeric(df[4,][c(2,3,4,5)])) ToPlot<-c(mean1,mean2,mean3,mean4) #plot barplot plot<-matrix(ToPlot,2,2,byrow=TRUE) #with 2 being replaced by the number of genes! tplot<-t(plot) BarPlot <- barplot(tplot, beside=TRUE,ylab="count", names.arg=c("Gene1","Gene2"),col=c("blue","red")) #add legend legend("topright", legend = c("SpeciesA","SpeciesB"), fill = c("blue","red")) #add error bars ee<-matrix(c(Gene1SpeciesA.stdev,Gene2SpeciesA.stdev,Gene1SpeciesB.stdev,Gene2SpeciesB.stdev),2,2,byrow=TRUE)*1.96/sqrt(4) tee<-t(ee) error.bar(BarPlot,tplot,tee) The problem is that I need to do this for 50
needs to be set at the layer level if you are overriding the plot defaults. data A layer specific dataset - only needed if you want to override the plot defaults. stat The statistical transformation to use on http://docs.ggplot2.org/0.9.3.1/geom_errorbar.html the data for this layer. position The position adjustment to use for overlappling points on this layer ... other arguments passed on to layer. This can include aesthetics whose values you want to set, not map. See layer for more details. Description Error bars. Aesthetics geom_errorbar understands the following aesthetics (required aesthetics are in bold): x ymax ymin alpha colour linetype size width Examples # Create a simple example error bars dataset df # Because the bars and errorbars have different widths # we need to specify how wide the objects we are dodging are dodge Mapping a variable to y and also using stat="bin". With stat="bin", it will attempt to set the y value to the count of cases in each group. This can result in unexpected behavior and will not be allowed in a future version of ggplot2. If with error bars you want y to represent counts of cases, use stat="bin" and don't map a variable to y. If you want y to represent values in the data, use stat="identity". See ?geom_bar for examples. (Deprecated; last used in version 0.9.2) p Mapping a variable to y and also using stat="bin". With stat="bin", it will attempt to set the y value to the count of cases in each group. This can result in unexpected behavior and will not be allowed in a future version of ggplot2. If you want y to represent counts of cases, use stat="bin" and don't map a variable to y. If you want y to represent values in the data, use stat="identity". See ?geom_bar for examples. (Deprecated; last used in version 0.9.2) p + geom_bar(position=dodge) + geom_errorbar(limits, position=dodge, width=0.25) Mapping a variable to y and also using stat="bin". With stat="bin", it will attempt to set the y value to the count of cases in each group. This can result in unexpected behavior and will not be allowed in a future version of ggplot2. If you want y to represent counts of cases, use stat="bin" and don't map a variable to y. If you want y to represent values in the data, use stat="identity". See ?geom_bar for examples. (Depr