Methods

plan %>% drake::vis_drake_graph(targets_only = T)

Abundance

loadd(abundance_heatmap_plot)
abundance_heatmap_plot

Intra feature type coabundances

Network properties

loadd(intra_feature_type_coabundances)

intra_feature_type_coabundances %>%
  mutate(
    n_nodes = coabundance %>% map_int(~ {
      .x %>% igraph::gorder()
    }),
    n_edges = coabundance %>% map_int(~ {
      .x %>%
        igraph::gsize() %>%
        as.integer()
    })
  ) %>%
  select(-coabundance) %>%
  filter(n_nodes > 0 | n_edges > 0) %>%
  arrange(-n_nodes, -n_edges) %>%
  knitr::kable()
disease feature_type method n_nodes n_edges
healthy pathway spearman 19 38
healthy pathway banocc 19 23
CRC pathway spearman 18 50
healthy taxon spearman 18 29
CRC pathway banocc 18 22
healthy taxon banocc 18 18
CRC taxon banocc 12 9
CRC taxon spearman 10 11
CRC taxon sparcc 5 3
healthy taxon sparcc 4 2

Networks

loadd(intra_feature_type_network_plots)

intra_feature_type_network_plots %<>%
  mutate(plot = list(plot, feature_type, disease) %>%
    pmap(~ ..1 + labs(title = paste0(..2, "-", ..3)))) %>%
  group_by(method) %>%
  do(plots = .$plot %>% wrap_plots() + plot_layout(guides = "collect")) %>%
  deframe()

Spearman

SparCC

BAnOCC

Node topology

content above tabbed region.

Spearman

SparCC

BAnOCC