Creating a Bubble Plot with ggplot2 and readxl in R

The input file can be downloaded here!

The code for creating the bubble plot above is written in R and utilizes the ggplot2 and readxl packages. It has the following steps:

1. Load required libraries: The ggplot2 library is used for data visualization, and the readxl library is used to read data from Excel files.

   library(ggplot2)
   library(readxl)
   

2. Read the data: The read_excel() function reads the data from the "WT.xlsx" file and stores it in the WT dataframe.

   WT <- read_excel("WT.xlsx")
   

3. Create the plot: The ggplot() function initializes the plot with the dataset (WT) and the aesthetics (Fold_Enrichment on the x-axis, reordered Term on the y-axis based on Log10FDR values).

   p = ggplot(WT, aes(Fold_Enrichment, reorder(Term, Log10FDR, order = TRUE)))
   

4. Add color and size to points: This step adds color to the points based on the "Log10FDR" variable and sets the size according to the "Count" variable.

   pbubble = p + geom_point(aes(size=Count, color=Log10FDR))
   

5. Customize the plot: This step sets the color gradient for points, labels the x-axis, and adjusts the size of the points.

   pr = pbubble + scale_color_gradient(low = "lightblue", high = "darkblue") +
     labs(x="Fold Enrichment", y="Term") +
     scale_size_continuous(range = c(1,10))
   

6. Increase font size of y-axis labels: The theme() function is used to increase the font size of y-axis labels (terms) to 12.

   pr = pr + theme_bw() + theme(axis.text.y = element_text(size = 12))
   

7. Save the plot: The png() function saves the plot as a PNG file with the specified dimensions, and the print() function prints the plot to the output file. The dev.off() function closes the graphics device, finalizing the output file.

   png("TFEB-wt24.png", width=700, height=500)
   print(pr)
   dev.off()
   

This code will generate a scatter plot with points colored and sized based on the "Log10FDR" and "Count" variables, respectively. The y-axis labels (terms) will be ordered according to the "Log10FDR" values and have an increased font size.

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