Failing to get individual boxplot intervals for sample locations for phylosq object

sondre brekkhus 0
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I have a phyloseq object containg an otu_table, tax_table and sam_data.physeq is the phyloseq object.

I want to use following code:

plot_richness(physeq, x ="Location" , measures = c("Observed", "Shannon")) + geom_boxplot()

Location is a column in sam_data with location 1,2,3 and 4, with each of my 100 samples associated with one location.

This is the plot i'm getting: One boxplot for observed and one for shannon. I want 4 boxplots in both.

I also keep geting a warning:

Warning message:
Continuous x aesthetic -- did you forget aes(group=...)?

I have seen identical code with the correct result without using aes.

phyloseq boxplot ggplot2 r
1 Answers

The warning message tells you that Location is a continuous numeric variable. You should convert Location to a factor or character before calling plot_richness Here's an example using GlobalPatterns.

require("phyloseq")
require("ggplot2")

# Load data
data("GlobalPatterns")
sample_data(GlobalPatterns)$Location <- sample(c(1, 2, 3, 4), nsamples(GlobalPatterns), replace = T)
plot_richness(GlobalPatterns, x = "Location", measures = c("Shannon", "Observed")) +
  geom_boxplot()
#> Warning: Continuous x aesthetic -- did you forget aes(group=...)?


# Update to factor
sample_data(GlobalPatterns)$Location <- as.factor(sample_data(GlobalPatterns)$Location)
plot_richness(GlobalPatterns, x = "Location", measures = c("Shannon", "Observed")) +
  geom_boxplot()

Created on 2022-09-08 by the reprex package (v2.0.1)

gmteunisse0
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