In R dealing with Error ggplot2 doesn t know how to deal with data of class numeric

Question

I m new to R and haven t done any programming before     When I attempt to create a box chart with standard error bars I get the error message mentioned in the title   I used a script I found on R Cookbook which I tweaked a bit   ggplot GVW  aes x  variable  y  value  fill  Genotype         geom bar position position dodge   stat  identity  colour  black   size  3     geom errorbar data GVW 1 64 3  aes ymin value-seSKO  ymax value seSKO   size  3  width  2  position position dodge  9      geom errorbar data GVW 65 131 3  aes ymin value-seSWT  ymax value seSWT   size  3  width  2  position position dodge  9      geom errorbar data GVW 132 195 3  aes ymin value-seEKO  ymax value seEKO   size  3  width  2  position position dodge  9      geom errorbar data GVW 196 262 3  aes ymin value-seEWT  ymax value seEWT   size  3  width  2  position position dodge  9      xlab  Time      ylab  Weight  g       scale fill hue name  Genotype   breaks c  KO    WT    labels c  Knock-out    Wild type       ggtitle  Effect of genotype on weight-gain      scale y continuous breaks 0 20 4      theme bw    Data lt - data frame    Genotype lt - sample c  KO   WT    262  replace T     variable lt - sample c  Start   End    262  replace T     value lt - runif 262 20 40    names Data  1   lt -  Genotype  names Data  2   lt -  variable  names Data  3   lt -  value

User · Accepted Answer

The error happens because of you are trying to map a numeric vector to data in geom_errorbar: GVW[1:64,3]. ggplot only works with data.frame.

In general, you shouldn't subset inside ggplot calls. You are doing so because your standard errors are stored in four separate objects. Add them to your original data.frame and you will be able to plot everything in one call.

Here with a dplyr solution to summarise the data and compute the standard error beforehand.

library(dplyr)
d <- GVW %>% group_by(Genotype,variable) %>%
    summarise(mean = mean(value),se = sd(value) / sqrt(n()))

ggplot(d, aes(x = variable, y = mean, fill = Genotype)) + 
  geom_bar(position = position_dodge(), stat = "identity", 
      colour="black", size=.3) +
  geom_errorbar(aes(ymin = mean - se, ymax = mean + se), 
      size=.3, width=.2, position=position_dodge(.9)) +
  xlab("Time") +
  ylab("Weight [g]") +
  scale_fill_hue(name = "Genotype", breaks = c("KO", "WT"), 
      labels = c("Knock-out", "Wild type")) +
  ggtitle("Effect of genotype on weight-gain") +
  scale_y_continuous(breaks = 0:20*4) +
  theme_bw()

[r] In R, dealing with Error: ggplot2 doesn't know how to deal with data of class numeric

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