Visualize one categorical column and one numeric column

Visualize one categorical column and one numeric column

plotByGroup(x, x.factor = NULL, y.numeric = NULL)

Arguments

x

phyloseq-class object.

x.factor

A column in sample_data to compare that is a factor

y.numeric

A column in sample_data to compare that is a numeric

Value

a ggplot object.

Details

A simple plotting utility for visualization of one categorical and numerical variable. Provided a categorical variable and numerical variable present in sample_data of a phyloseq-class object, a comparative visualization can be done.

References

Shetty SA (2021). Data visualization for microbiome analytics. https://github.com/microsud/biomeViz

Author

Sudarshan A. Shetty

Examples

library(biomeUtils)
library(biomeViz)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(microbiome)
library(ggplot2)
ps <- FuentesIliGutData
# calculate Shannon diversity using microbiome::diversity and add it to
# the sample_data in phyloseq using biomeUtils::mutateSampleData()
ps <- mutateSampleData(ps,
                       Shannon = microbiome::diversity(ps, "shannon")[,1])
plotByGroup(ps,
            x.factor="ILI",
            y.numeric = "Shannon") +
         geom_point(aes(color=ILI),
                    position = position_jitter(width = 0.1)) +
         scale_color_manual(values=c("steelblue", "brown3", "grey70"))