inst/doc/beta_diversity_ordinations.R

In HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis

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library(dplyr)
library(ggplot2)
library(HTSSIP)

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physeq_S2D2

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params = get_treatment_params(physeq_S2D2, c('Substrate', 'Day'))
params

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params = dplyr::filter(params, Substrate!='12C-Con')
params

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ex = "(Substrate=='12C-Con' & Day=='${Day}') | (Substrate=='${Substrate}' & Day == '${Day}')"
physeq_S2D2_l = phyloseq_subset(physeq_S2D2, params, ex)
physeq_S2D2_l

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# running in parallel
doParallel::registerDoParallel(2)
physeq_S2D2_l_df = SIP_betaDiv_ord(physeq_S2D2_l, parallel=TRUE)
physeq_S2D2_l_df %>% head(n=3)

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physeq_S2D2_l_df %>% .$phyloseq_subset %>% unique

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physeq_S2D2_l_df = physeq_S2D2_l_df %>%
  dplyr::mutate(phyloseq_subset = gsub(' \\| ', '\n', phyloseq_subset),
                phyloseq_subset = gsub('\'3\'', '\'03\'', phyloseq_subset))
physeq_S2D2_l_df %>% .$phyloseq_subset %>% unique

## ---- fig.height=6, fig.width=7.5----------------------------------------
phyloseq_ord_plot(physeq_S2D2_l_df)

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sessionInfo()