st_evolution: Generate boxplots of the stability evolution throughout...

In microSTASIS: Microbiota STability ASsessment via Iterative cluStering

Description

Generate boxplots of the stability evolution throughout sampling times by groups

Usage

st_evolution(data, groups = NULL, points = TRUE, linetype = 2)

Arguments

data	input data frame resulting from st_previz().
groups	vector with the same length as the number of rows in the st_previz() output.
points	logical; FALSE to only visualize boxplots or TRUE to also add individual points.
linetype	numeric; type of line to connect the median value of paired times; 0 to avoid the line.

Value

A plot with as many boxes as paired times by group in the form of a "ggplot" object.

Examples

t1_t2 <- paired_times(data = clr[,1:25], first = "_1",
                      second = "_25", common = "_0_")
t2_t3 <- paired_times(data = clr[,1:25], first = "_25",
                      second = "_26", common = "_0_")
klist_t1_t2 <- iterative_clustering(data = t1_t2, parallel = FALSE)
klist_t2_t3 <- iterative_clustering(data = t2_t3, parallel = FALSE)
result_t1_t2 <- stabilitas(klist_t1_t2, common = "_0_")
result_t2_t3 <- stabilitas(klist_t2_t3, common = "_0_")
results <- st_previz(results = list(result_t1_t2, result_t2_t3),
                     times = c("t1_t2", "t2_t3"))
metadata <- data.frame(Sample = rownames(clr),
                       age = c(rep("youth", 65), rep("old", 131-65)))
group <- metadata_groups(metadata = metadata, samples = metadata$Sample,
                         individuals = results$individual, col_number = 2)
st_evolution(results, groups = group, points = TRUE, linetype = 0)

microSTASIS documentation built on Sept. 14, 2021, 9:07 a.m.