Bar Plots R Error Bars
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Barplot With Error Bars Matlab
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Calculate Standard Error In R
Discuss the workings and policies of this site About Us Learn r arrows more about Stack Overflow the company Business Learn more about hiring developers or posting ads with us plot mean and standard deviation in r 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, https://www.r-bloggers.com/building-barplots-with-error-bars/ 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 http://stackoverflow.com/questions/29768219/grouped-barplot-in-r-with-error-bars 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 t
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 http://stackoverflow.com/questions/29995480/side-by-side-r-barplot-with-error-bars this site About Us Learn more about Stack Overflow the company Business http://rstatistics.tumblr.com/post/470327991/make-a-barplot-with-errorbars-now-this-is-a 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 error bars up Side by Side R Barplot with error bars up vote 0 down vote favorite say I have the means of two datasets that I want to plot as barplots with error bars next to each other in ggplot2, or base Each dataset consists of a matrix of numbers 10 20 12 10 20 12 10 20 12 which is then transformed into barplot with error a mean vector of for example 3 elements 10 20 12 What I want to do is to take both mean vectors and plot them as a bar plot where the first element of one is besides the first element of the other Dataset1Element1Bar-Dataset2Element1Bar Dataset1Element2Bar-Dataset2Element2Bar etc Give each bar an error bar, say of standard deviation. I know I can calculate it through sd but I'm not sure how to stick it into the graph in the proper form And lastly color them by their element number (ie Element 1) I have the code to do one dataset but I'm not sure where to go from there. result<-barplot(bardata, main="Mean Coverage", names.arg=namePosTargetGroup, ylab="mean Magnitude", cex.names=.4,col=c("red","blue","green")) legend(10,legend=c("Group1","Group2","Group3"),fill = c("red","blue","green")) A lot of what I look up gives the answer for one thing or another but its difficult to figure out how to combine them together. r graph plot ggplot2 share|improve this question asked May 1 '15 at 21:33 A D 328 add a comment| 1 Answer 1 active oldest votes up vote 1 down vote I would generally not recommend plotting just a bar chart with error bars.
a barplot with errorbars Now this is a tricky one: I wrote a script to plot a barplot with errorbars. I used the following script: #barplot where x is the independent on the x-axis, y is the #dependent on the y-axis and z is the independent given by #different colored bars anova.plot<-function(x, y, z, ylab="y", xlab="x", ylim=c(0, max(xx)+max(yy)), length=0.05){ #height of the bars xx<-tapply(y,list(z,x),mean) #standard deviation yy<-tapply(y,list(z,x),sd) #number of replicates zz<-tapply(y,list(z,x),length) #standard error er<-yy/sqrt(zz) #number of colors for bars w<-length(levels(z)) #simple barplot without the errorbars barx<-barplot(xx, col=c(1:w), beside=T, ylab=ylab, xlab=xlab, ylim=ylim,xpd=FALSE) #box around the plot box() #error bars arrows(barx,xx+er, barx, xx, angle=90, code=1, length=length) #legend (after making the plot, indicate where the legend has #to come with the mouse) legend(locator(1),c(levels(z)),fill=c(1:w),bty="n",cex=0.8) } If you have set your palette to: palette(c("grey25","grey50","grey75","white")) you get a plot like the one above if you use: anova.plot(x,y,z) (6 years ago) archive : rss : theme "2001" by 54mf : powered by Tumblr