Error Bars R Ggplot2
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needs to be set at the layer level if you are overriding the plot defaults. data A layer specific dataset - only needed if you ggplot2 barplot with error bars want to override the plot defaults. stat The statistical transformation to
Ggplot2 Points With Error Bars
use on the data for this layer. position The position adjustment to use for overlappling points on this ggplot error bars 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 summaryse r 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 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
R Calculate Standard Error
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 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=dod
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Error Bars In R
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here for a quick overview of the site Help Center Detailed answers to any questions you might have Meta Discuss the workings and policies of this site About Us Learn more about Stack http://stackoverflow.com/questions/15064462/r-ggplot2-barplot-and-error-bar Overflow the company Business Learn more about hiring developers or posting ads with us http://stackoverflow.com/questions/29768219/grouped-barplot-in-r-with-error-bars 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 minute: Sign up R: ggplot2 barplot and error bar up vote 2 down vote favorite Since the new error bars version of ggplot2 (0.9.3), I've problem to plot barplots with errorbars. So I've a dataframe like this : group N val sd se ci 1 206 3 37.2269533 7.9688645 4.6008261 19.7957568 2 207 3 2.0731505 2.2843009 1.3188417 5.6745180 3 208 3 2.2965978 1.4120606 0.8152536 3.5077531 4 209 3 3.1085132 1.1986664 0.6920504 2.9776525 5 210 3 3.3735251 1.9226134 1.1100214 4.7760365 6 211 3 4.0477951 2.9410503 1.6980162 7.3059739 7 212 3 1.2391158 1.2345554 with error bars 0.7127709 3.0668055 8 213 2 1.3082374 1.1234220 0.7943793 10.0935460 I want to plot for each group the val +- s : I did that before upgrade : ggplot(dfc, aes(x=factor(group), y=factor(val)) + geom_bar(position=position_dodge()) + geom_errorbar(aes(ymin=val-se, ymax=val+se),width=.1,position=position_dodge(.9)) It gives me that: 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) So anyone knows how to resolve that ? Thanks N. r ggplot2 share|improve this question asked Feb 25 '13 at 10:06 NicoBxl 3374515 add a comment| 1 Answer 1 active oldest votes up vote 6 down vote accepted Is this what you're after? my.df <- read.table(text = "group N val sd se ci 206 3 37.2269533 7.9688645 4.6008261 19.7957568 207 3 2.0731505 2.2843009 1.3188417 5.6745180 208 3 2.2965978 1.4120606 0.8152536 3.5077531 209 3 3.1085132 1.1986664 0.6920504 2.9776525 210 3 3.3735251 1.9226134 1.1100214 4.7760365 211 3 4.0477951 2.9410503 1
here for a quick overview of the site Help Center Detailed answers to any questions you might have Meta Discuss the workings and policies of this site About Us Learn more about Stack Overflow the company Business Learn more about hiring developers or posting 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 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 genes, and 4 species, so my script is gonna get super super long and I guess this is not optimized... I tried to find help here but I can't figure out a better way to do what I'd like. If I did not need error bars I could adapt this script but the tricky part is to mix ggplot beautiful barplots and error bars! ;) If you have any idea to optimize my script, I would really appreciate! :) Thanks a lot! r ggplot2 bar-chart share|improve this question asked Apr 21 '15 at 9:32 tlorin 173213 1 beware by doing t(plot) you completely inversed the gene ;) –Colonel Beauvel Apr 21 '15 at 11:36 add a comment| 1 Answer 1 active oldest votes up vote