Reorder GO terms using R

Question

[hellokwmin]

Hello,

I plotted my GO data using this code:

ggplot(result_ego_filtered, aes(Count, Description, fill = ONTOLOGY)) +
  geom_bar(stat = "identity") +
  theme(legend.position = "bottom", axis.title.y = element_blank()) +
  geom_text(
    aes(label = paste(Count)),
    color = "black",
    size = 4,
    hjust = 0.1,
    position = position_dodge(0.9)
  )

And, I've got this plot:

How could I reorder ontology? I would like to show BP together followed by MF, and CC.

[Mark]

Check the package forcats to manually reorder the GO terms https://forcats.tidyverse.org/reference/fct_relevel.html

Answer 1

[Papyrus]

To order things in ggplot2, you use factors and specify factor levels as the order. The key thing in your example is that you actually want to order your pathways: your y variable (Description), based on your database: your fill variable (ONTOLOGY).

A solution could be to:

1. specify the database (ONTOLOGY) variable as a factor where the levels are the desired order (you could use forcats for this as Mark suggests)
2. arrange your input data by this database factor with dplyr::arrange
3. speficy the pathway (Description) variable as a factor where the levels are the final order in which they are

For example:

# Libraries
library(ggplot2)
library(dplyr)

# Example data
data <- data.frame(
  Description = c("A","E","B","I","O","J","K"),
  ONTOLOGY = c("BP","MF","BP","MF","CC","BP","CC"),
  Count = sample(1:10,7)
)

# Your initial plot
ggplot(data, aes(Count, Description, fill = ONTOLOGY)) + geom_bar(stat = "identity") +
  theme(legend.position = "bottom", axis.title.y = element_blank()) +
  geom_text( aes(label = paste(Count)), color = "black", size = 4, hjust = 0.1, position = position_dodge(0.9) )

# Define the order for the ontology types (BP, MF, CC)
data$ONTOLOGY <- factor(data$ONTOLOGY, levels = rev(c("BP","MF","CC")))

# Arrange the dataframe by the ontology types
data <- dplyr::arrange(data, ONTOLOGY)

# Set the final factor order for the pathways
data$Description <- factor(data$Description, levels = data$Description)

# Final ordered plot
ggplot(data, aes(Count, Description, fill = ONTOLOGY)) + geom_bar(stat = "identity") +
  theme(legend.position = "bottom", axis.title.y = element_blank()) +
  geom_text( aes(label = paste(Count)), color = "black", size = 4, hjust = 0.1, position = position_dodge(0.9) )

[hellokwmin]

Thank you so much. It worked perfectly.