Ggplot2 bar graph a closure object is not a subset

Question

I use the data that I have here.

I summarize the data and then want to use this to build a histogram.

Here is my code:

heights<-read.csv("reading_anthesis.csv",as.is=T)
str(heights)
##DATA SUMMARY##
##code for data summary from 
## http://www.cookbook-r.com/Manipulating_data/Summarizing_data/
##    data: a data frame.
##   measurevar: the name of a column that contains the variable to be summariezed
##   groupvars: a vector containing names of columns that contain grouping variables
##   na.rm: a boolean that indicates whether to ignore NA's
##   conf.interval: the percent range of the confidence interval (default is 95%)


summarySE <- function(data=NULL, measurevar, groupvars=NULL, na.rm=FALSE,
                      conf.interval=.95, .drop=TRUE) {
  require(plyr)

  # New version of length which can handle NA's: if na.rm==T, don't count them
  length2 <- function (x, na.rm=FALSE) {
    if (na.rm) sum(!is.na(x))
    else       length(x)
  }

  # This does the summary. For each group data frame, return a vector with
  # N, mean, and sd
  datac <- ddply(data, groupvars, .drop=.drop,
                 .fun = function(xx, col) {
                   c(N    = length2(xx[[col]], na.rm=na.rm),
                     mean = mean   (xx[[col]], na.rm=na.rm),
                     sd   = sd     (xx[[col]], na.rm=na.rm)
                   )
                 },
                 measurevar
  )

  # Rename the "mean" column    
  datac <- rename(datac, c("mean" = measurevar))

  datac$se <- datac$sd / sqrt(datac$N)  # Calculate standard error of the mean

  # Confidence interval multiplier for standard error
  # Calculate t-statistic for confidence interval: 
  # e.g., if conf.interval is .95, use .975 (above/below), and use df=N-1
  ciMult <- qt(conf.interval/2 + .5, datac$N-1)
  datac$ci <- datac$se * ciMult

  return(datac)
}


summary<-summarySE(heights, measurevar="height", groupvars=c("genotype", "treatment"))
summary.2<-summary
summary.2$genotype<-factor(summary.2$genotype)
summary.2$treatment<-factor(summary.2$treatment)

pd <- position_dodge(.9)
ggplot(summary.2, aes(x=genotype, y=height, fill=genotype)) + 
  geom_bar(position=position_dodge(), stat=identity, colour ="black") +
  geom_errorbar(aes(ymin=height-se, ymax=height+se), colour="black", width=.3, position=pd) +
  ylab("Height (cm)") +
  theme(axis.title = element_text(size=14,face="bold"), 
        axis.text = element_text(size=13),
        strip.text.y = element_text(size=12))

I get an error message: Error in stat$parameters : object of type 'closure' is not subsettable

And I cannot find where I have a function / vector that I did not define, as the previous messages were implied.

Very grateful for any help.

Answer 1

The problem was trivial, but tracking it is really a difficult task. stat=identityshould be stat="identity". I also changed fill=treatmentto get the following image:

ggplot(summary.2, aes(x=genotype, y=height, fill=treatment)) + 
    geom_bar(position=position_dodge(), stat="identity", colour="black") +
    geom_errorbar(aes(ymin=height-se, ymax=height+se), 
                  colour="black", width=.3, position=pd) +
    ylab("Height (cm)") +
    theme(axis.title = element_text(size=14, face="bold"), 
          axis.text = element_text(size=13),
          strip.text.y = element_text(size=12))