Error in eval(expr, envir, enclos) : object 'variable' not found- ggplot2

Question

I need help to make the ggplot2 plot for my data. This is my script in R.

> library(reshape2)
> library(ggplot2)
mdat = read.csv(file = "~/Desktop/final_data/low_group.csv", header = TRUE, sep="\t") 
> head(mdat)
         day..variable..value
1 Day 0, Actinobacteria,0.187
2 Day 3, Actinobacteria,0.117
3 Day 6, Actinobacteria,0.153
4 Day 9, Actinobacteria,0.147
5  Day 0, Bacteroidetes,0.154
6  Day 3, Bacteroidetes,0.364
> ggplot(mdat, aes(variable, value, fill=day)) + 
+     geom_bar(stat="identity", position="dodge") +
+     scale_alpha_discrete(range = c(0.5,1)) +
+     theme_minimal()
Error in eval(expr, envir, enclos) : object 'variable' not found

Any suggestion please!! Thank you very much.

That error means you don't have a column named variable in your dataframe. Look at what names(mdat) prints. It looks like you told read.csv that your file was tab-delimited when in fact it was probably comma-delimited — camille
+1 what Camille said above; it looks like day..variable..value is a single column name, and your data has one column. Try also dim(mdat) to check this, and replace sep="\t" with sep="" or nothing to split the data with commas — Scransom

Claus Wilke Claus Wilke · Accepted Answer · 2018-04-27T04:05:27

As was mentioned in comments, the problem is that you have a comma-separated file (csv) but you're reading it as if it where tab-separated. I can reproduce your problem and then rectify it by reading the file correctly.

First, I create a simple csv file:

df <- data.frame(day = c("Day 0", "Day 3", "Day 6"),
                 variable = c("Actinobacteria", "Actinobacteria", "Actinobacteria"),
                 value = c(0.187, 0.117, 0.153))
write.table(df, "low_group.csv", row.names = FALSE, sep = ", ")

Now, I read it in the way you do, with sep="\t" (tab-separated). The tell-tale sign that something is wrong is in the column header, day..variable..value, which is a single string, hence the data frame mdat contains only a single column:

mdat <- read.csv(file = "low_group.csv", header = TRUE, sep="\t") 
head(mdat)
#           day..variable..value
# 1 Day 0, Actinobacteria, 0.187
# 2 Day 3, Actinobacteria, 0.117
# 3 Day 6, Actinobacteria, 0.153

If we try to plot this we get an error. (My error message is slightly different because I run the development version of ggplot2.)

ggplot(mdat, aes(variable, value, fill=day)) + geom_col()
# Error in FUN(X[[i]], ...) : object 'variable' not found

Now let's do it correctly, without sep="\t". Now we get three separate columns in the data frame, and we can plot them.

mdat <- read.csv(file = "low_group.csv", header = TRUE) 
head(mdat)
#     day        variable value
# 1 Day 0  Actinobacteria 0.187
# 2 Day 3  Actinobacteria 0.117
# 3 Day 6  Actinobacteria 0.153
ggplot(mdat, aes(variable, value, fill=day)) + geom_col()

Error in eval(expr, envir, enclos) : object 'variable' not found- ggplot2

2 Answers