ps_reorder: Set order of samples in phyloseq object

In david-barnett/microViz: Microbiome Data Analysis and Visualization

Set order of samples in phyloseq object

Description

Manually set order of samples by specifying samples names in desired order.

Usage

ps_reorder(ps, sample_order)

Arguments

ps	phyloseq
sample_order	names or current numerical indices of samples in desired order

Details

Ordering of samples in a phyloseq is controlled from the otu_table slot!

Value

phyloseq

See Also

ps_arrange for arranging samples by sample_data variables (or otu_table)

ps_seriate for arranging samples by microbiome similarity

ps_filter for keeping only some samples, based on sample_data

Examples

library(phyloseq)
data("dietswap", package = "microbiome")

dietswap %>%
  sample_data() %>%
  head(8)

new_order <- rev(sample_names(dietswap))
dietswap %>%
  ps_reorder(new_order) %>%
  sample_data() %>%
  head(8)

# random ordering with numbers
set.seed(1000)
random_order <- sample(1:nsamples(dietswap))
dietswap %>%
  ps_reorder(random_order) %>%
  sample_data() %>%
  head(8)

david-barnett/microViz documentation built on April 17, 2025, 4:25 a.m.