Plot Longitudinal Taxa Trajectories

Plot selected taxa across an ordered sample metadata variable.

Usage

plot_longitudinal(
  object,
  taxonomic_rank = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"),
  time_by,
  id_by = NULL,
  color_by = NULL,
  taxa = NULL,
  top_n = 6,
  relative = TRUE
)

Arguments

object

A microbiome_dataset object.

taxonomic_rank

Taxonomic rank used for aggregation.

time_by

Sample metadata column used on the x axis.

id_by

Optional metadata column used to connect repeated measures.

color_by

Optional metadata column used for color.

taxa

Optional taxa labels.

top_n

Number of taxa shown when taxa is omitted.

relative

Whether to use relative abundance.

Value

A ggplot object.

Examples

data("demo_crossomics", package = "microbiomedataset")
plot_longitudinal(
  demo_crossomics$microbiome_data,
  taxonomic_rank = "Genus",
  time_by = "age",
  id_by = "subject_id",
  top_n = 4
)
#> `geom_line()`: Each group consists of only one observation.
#> ℹ Do you need to adjust the group aesthetic?
#> `geom_line()`: Each group consists of only one observation.
#> ℹ Do you need to adjust the group aesthetic?
#> `geom_line()`: Each group consists of only one observation.
#> ℹ Do you need to adjust the group aesthetic?
#> `geom_line()`: Each group consists of only one observation.
#> ℹ Do you need to adjust the group aesthetic?