Hey there, let's break down why you're hitting that error and get your plot working smoothly!

The Root Cause #

Looking at your head(mdat) output, you'll notice all your data is crammed into a single column named day..variable..value. That's because you used sep="\t" (tab delimiter) when reading your CSV, but your actual data is separated by commas (e.g., Day 0, Actinobacteria,0.187). Since R couldn't split the data into separate columns, it has no idea what variable, day, or value are—hence the "object not found" error.

Step-by-Step Fix #

1. Correctly Read Your Data
   First, fix the read.csv call to use the right delimiter. Since your data uses commas, you can either explicitly set sep="," or just rely on read.csv's default (it uses commas by default):

   library(reshape2)
   library(ggplot2)
   
   # Read with correct comma delimiter
   mdat <- read.csv(file = "~/Desktop/final_data/low_group.csv", header = TRUE)
   
   # Optional: If column names still look wonky, manually rename them
   colnames(mdat) <- c("day", "variable", "value")
   

2. Verify Your Data Structure
   Run str(mdat) to confirm you have three distinct columns:

   • day: Character/factor (e.g., "Day 0", "Day 3")
   • variable: Character/factor (e.g., "Actinobacteria", "Bacteroidetes")
   • value: Numeric (the abundance values)

3. Plot with ggplot2
   Now that your columns are properly separated, your original plot code will work. Here's a polished version with clear labels and a clean theme:

   ggplot(mdat, aes(x = variable, y = value, fill = day)) +
     geom_bar(stat = "identity", position = "stack") + # Stacked bars (default, but explicit is clear)
     labs(
       title = "Microbial Relative Abundance by Day",
       x = "Microbial Phylum",
       y = "Relative Abundance",
       fill = "Sampling Day"
     ) +
     theme_bw() +
     theme(axis.text.x = element_text(angle = 45, hjust = 1)) # Rotate x-axis labels for readability
   

Quick Tips for Future Plots #

• Always double-check your data's delimiter before reading it into R (commas, tabs, and spaces are the most common).
• Use str(mdat) or summary(mdat) to confirm your variables are the right type (numeric columns shouldn't be stored as characters!).

内容的提问来源于stack exchange，提问作者Susie