Hey Lisa, let’s sort out this tricky Y-axis ordering problem once and for all— dealing with categorical ordering in ggplot can be frustrating, especially when you’ve got 100+ species to wrangle. Here’s a straightforward solution that will keep your species in taxonomic order while displaying their proper names on the Y-axis:

Core Solution: Use Ordered Factors #

The key is to convert your Species column into an ordered factor that locks in the taxonomic order based on your Number column. This way, ggplot will respect the order automatically, no messy scale_y_discrete hacks needed.

Step 1: Define the Species Order #

First, extract the unique pairing of Number and Species, then sort them to match your desired taxonomic sequence (since your Number column is set to maintain this order):

# Load dplyr if you haven't already (for data manipulation)
library(dplyr)

# Get unique Species-Number pairs, sorted by Number (adjust desc() if you need reverse order)
species_order <- data %>%
  distinct(Number, Species) %>%
  arrange(desc(Number)) %>% # Use arrange(Number) if you want Number ascending at the top
  pull(Species)

• The desc(Number) ensures species with higher Number values (like your Grey francolin with 142) appear at the top of the Y-axis, matching your taxonomic order.
• distinct() removes duplicate entries so we only get one row per species.

Step 2: Convert Species to an Ordered Factor #

Update your data frame to turn Species into a factor with the order we just defined:

data$Species <- factor(data$Species, levels = species_order, ordered = TRUE)

This tells R to treat Species as a categorical variable with a fixed, non-alphabetical order.

Step 3: Update Your ggplot Code #

Now you can directly use Species on the Y-axis— ggplot will follow the factor's order and display the species names correctly:

library(ggplot2)

ggplot(data, aes(x = Sample, y = Species)) +
  geom_point(aes(size = ifelse(Value == 0, NA, Value), alpha = 0.75)) +
  scale_size(range = c(0, 5))

Why Your Previous Approach Didn’t Work #

When you used y = Number (a numeric column) and tried to overwrite labels with scale_y_discrete(limits = c(data$Species)), ggplot was confused:

• It was treating the Y-axis as numeric first, then trying to map discrete labels to numeric positions, which causes misalignment.
• Using c(data$Species) passed a vector with duplicate species names, which ggplot would automatically deduplicate but reorder alphabetically behind the scenes.

Bonus: Troubleshooting for Large Datasets #

Since you have over 100 species, this method scales perfectly:

• distinct() and arrange() handle large data frames efficiently.
• The ordered factor preserves your taxonomic order through any subsequent data filtering or manipulation.

内容的提问来源于stack exchange，提问作者Lisa B