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Working on LBM seq analysis

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Louis 2026-02-09 17:50:07 +01:00
parent 691ad05b25
commit 20d26e8634
1 changed files with 34 additions and 6 deletions
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38
analysis_benchmark_lbm_seq.qmd
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@ -203,14 +203,42 @@ ggplot(seq_df_otu_lodes, aes(x = x, alluvium = alluvium, stratum = stratum, labe
```
```{r}
ARI_ranks <- function(df_otu) {
list_memberships <- function(df_otu) {
memb_mat <- df_otu |> select(starts_with("Z"))
memb_list <- lapply(seq_len(ncol(memb_mat)), function(i) memb_mat[,i] |> unlist() |> as.vector())
outer(memb_list,memb_list, FUN = Vectorize(ARI))}
ARI_ranks(seq_df_otu)
ARI_ranks(notrans_df_otu)
memb_list <- lapply(seq_len(ncol(memb_mat)), function(i) {
memb_mat[, i] |>
unlist() |>
as.vector()
})
return(memb_list)
}
seq_memb_list <- list_memberships(seq_df_otu)
notrans_memb_list <- list_memberships(notrans_df_otu)
outer(seq_memb_list, seq_memb_list, Vectorize(ARI))
outer(notrans_memb_list, notrans_memb_list, Vectorize(ARI))
```
### ARI phylogénie et clustering
```{r}
phylo_df <- data.frame(merged = rownames(tail(per_taxa_networks, 1)[[1]])) %>% separate(col = "merged", into = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"), sep = ";_;")
phylo_df <- phylo_df %>% rename_all(~ str_c("Rank", which(colnames(phylo_df) == .)))
phylo_df <- phylo_df %>% mutate_all(as.factor)
phylo_memb_list <- lapply(seq_len(ncol(phylo_df)), function(i) {
phylo_df[, i] |>
unlist() |>
as.factor()
})
outer(phylo_memb_list, , Vectorize(ARI))
```
## ICL
```{r}
# Extract ICL
ICL_per_ranks <- function(model_results) {