R 中带有误差条的分组条形图 [英] Grouped barplot in R with error bars

问题描述

我想绘制一个带有误差线的分组条形图.这是我到目前为止能够得到的那种数字，这对于我需要的来说是可以的:

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:

这是我的脚本:

#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)

问题是我需要为 50 个基因和 4 个物种做这个，所以我的脚本会变得超长而且我猜这没有优化......我试图寻求帮助 这里 但我想不出更好的方法来做我想做的事.如果我不需要错误栏，我可以调整这个脚本，但棘手的部分是混合 ggplot 漂亮的条形图和误差条！;)

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! ;)

如果您有任何优化我的脚本的想法，我将不胜感激！:)

If you have any idea to optimize my script, I would really appreciate! :)

非常感谢！

推荐答案

从你对 df 的定义开始，你可以用几行来完成:

Starting from your definition of df, you can do this in a few lines:

library(ggplot2)

cols = c(2,3,4,5)
df1  = transform(df, mean=rowMeans(df[cols]), sd=apply(df[cols],1, sd))

# df1 looks like this
#   Gene count1 count2 count3 count4 Species  mean        sd
#1 Gene1     12      4     36     12       A 16.00 13.856406
#2 Gene2     14      7     22     24       A 16.75  7.804913
#3 Gene1     16      9     54     35       B 28.50 20.240224
#4 Gene2     34     23     12     23       B 23.00  8.981462

ggplot(df1, aes(x=as.factor(Gene), y=mean, fill=Species)) +
  geom_bar(position=position_dodge(), stat="identity", colour='black') +
  geom_errorbar(aes(ymin=mean-sd, ymax=mean+sd), width=.2,position=position_dodge(.9))

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