191 lines
No EOL
6.3 KiB
Text
191 lines
No EOL
6.3 KiB
Text
---
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title: "Stats at Taxo"
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format: html
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---
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```{r}
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library(here)
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library(stringr)
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library(tidyverse)
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library(phyloseq)
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library(biomformat)
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source("utils.R")
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the_data <- import_biom("data/mach/kinetic.biom")
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per_taxa_networks <- collapse_otu_at_taxo(the_data)
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otu_df <- sapply(per_taxa_networks, nrow) %>%
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data.frame() %>%
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rownames_to_column() %>%
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rename(Nb_OTU = ".", Rank = "rowname")
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flist <- list.files(here("results", "lbm-seq"), full.names = TRUE, pattern = ".Rds")
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para_flist <- grepv(pattern = "para.Rds", flist)
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seq_flist <- grepv(pattern = "seq.Rds", flist)
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notrans_flist <- grepv(pattern = "notrans.Rds", flist)
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```
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```{r}
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bench_df <- do.call("rbind", lapply(flist, function(file) readRDS(file)$benchmark))
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bench_df <- bench_df %>%
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mutate(expr = as.character(expr)) %>%
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separate_wider_regex(cols = "expr", patterns = c(Rank = "Rank[0-9]", type = "para|seq|notrans")) %>%
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mutate(Rank = as.factor(Rank), type = as.factor(type)) %>%
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left_join(otu_df, by = "Rank") %>%
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mutate(Rank = as.factor(Rank), type = as.factor(type))
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levels(bench_df$Rank) <- c("Phylum", "Class", "Order", "Family", "Genus")
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```
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```{r}
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library(ggplot2)
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coeff <- 220000000000
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ggplot(bench_df, aes(x = Rank, col = type)) +
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geom_boxplot(aes(y = time)) +
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geom_point(aes(y = coeff * Nb_OTU, size = Nb_OTU), shape = 13) +
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scale_color_manual(values = c("#363634", "#009E73", "#CC79A7"), labels = c("No transfer", "Parallelized", "Sequential")) +
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scale_y_continuous(sec.axis = sec_axis(~ . / coeff, name = "Number of OTUs")) +
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labs(size = "Number of OTUs", color = "Algorithm Type", y = "Time (seconds)") +
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theme_minimal()
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```
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```{r}
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load_result_list <- function(flist) {
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results <- lapply(flist, function(file) readRDS(file)$models)
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names(results) <- paste0("Rep", seq_along(results))
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results <- purrr::transpose(results)
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return(results)
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}
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library(aricode)
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ARI_in_repet_Z1 <- function(result_list) {
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lapply(result_list, function(rank) {
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Z1_list <- lapply(rank, function(repet) {
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Z11 <- apply(repet$memberships[[which.max(repet$ICL)]]$Z1, 1, which.max)
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})
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outer(X = Z1_list, Y = Z1_list, Vectorize(ARI))
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})
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}
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ARI_in_repet_Z2 <- function(result_list) {
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lapply(result_list, function(rank) {
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Z2_list <- lapply(rank, function(repet) {
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Z2 <- apply(repet$memberships[[which.max(repet$ICL)]]$Z2, 1, which.max)
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})
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outer(X = Z2_list, Y = Z2_list, Vectorize(ARI))
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})
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}
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```
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```{r}
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seq_results <- load_result_list(seq_flist)
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para_results <- load_result_list(para_flist)
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notrans_results <- load_result_list(notrans_flist)
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```
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```{r}
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ARI_in_repet_Z1(seq_results)
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ARI_in_repet_Z1(para_results)
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ARI_in_repet_Z1(notrans_results)
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```
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```{r}
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ARI_in_repet_Z2(seq_results)
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ARI_in_repet_Z2(para_results)
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ARI_in_repet_Z2(notrans_results)
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```
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Tous les Z sont concordants entre les répétitions, je vais donc sélectionner une seule répétition de chaque pour l'analyse.
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# Analyse des résultats des LBM
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Ci-après on extrait les premiers modèles.
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```{r}
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seq_model <- purrr::transpose(seq_results)[[2]]
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para_model <- purrr::transpose(para_results)[[1]]
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notrans_model <- purrr::transpose(notrans_results)[[1]]
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```
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```{r}
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extract_memberships <- function(model) {
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memberships <- model$memberships[[which.max(model$ICL)]]
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rownames(memberships[["Z1"]]) <- rownames(model$adj)
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rownames(memberships[["Z2"]]) <- colnames(model$adj)
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memberships
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map_memberships <- list(Z1 = apply(memberships[["Z1"]], 1, which.max), Z2 = apply(memberships[["Z2"]], 1, which.max))
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map_memberships
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}
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```
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## Comparaison des ARI par rang taxonomique
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```{r}
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seq_memberships <- lapply(seq_model, extract_memberships)
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para_memberships <- lapply(para_model, extract_memberships)
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notrans_memberships <- lapply(notrans_model, extract_memberships)
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```
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```{r}
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tibble("Para v No transfer" = map2_dbl(purrr::transpose(para_memberships)[["Z1"]], purrr::transpose(notrans_memberships)[["Z1"]], .f = ARI), "Sequential v No transfer" = map2_dbl(purrr::transpose(seq_memberships)[["Z1"]], purrr::transpose(notrans_memberships)[["Z1"]], .f = ARI), "Para v Sequential" = map2_dbl(purrr::transpose(para_memberships)[["Z1"]], purrr::transpose(seq_memberships)[["Z1"]], .f = ARI)) %>% t() %>%
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knitr::kable(col.names = paste0("Rank", seq(2,5)), caption = "ARI for the methods for OTU memberships")
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```
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```{r}
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tibble("Para v No transfer" = map2_dbl(purrr::transpose(para_memberships)[["Z2"]], purrr::transpose(notrans_memberships)[["Z2"]], .f = ARI), "Sequential v No transfer" = map2_dbl(purrr::transpose(seq_memberships)[["Z2"]], purrr::transpose(notrans_memberships)[["Z2"]], .f = ARI), "Para v Sequential" = map2_dbl(purrr::transpose(para_memberships)[["Z2"]], purrr::transpose(seq_memberships)[["Z2"]], .f = ARI)) %>% t() %>%
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knitr::kable(col.names = paste0("Rank", seq(2,5)), caption = "ARI for the methods for sample memberships")
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```
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```{r}
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library(ggalluvial)
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membership_to_df <- function(membership_list, suffix = 1) {
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lapply(membership_list, function(membership_vec) {
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df <- data.frame(membership_vec)
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colnames(df) <- paste0("Z", suffix)
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df %>%
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rownames_to_column(var = "Rank") %>%
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separate_wider_delim(cols = "Rank", delim = ";_;", names_sep = "")
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})
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}
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seq_df <- lapply(seq_along(seq_memberships), function(idx) {
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membership_to_df(seq_memberships[[idx]], suffix = idx + 1)
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})
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seq_df_otu <- lapply(seq_df, function(df) {
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df$Z1
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}) %>% # Below we join by the ranks
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reduce(left_join) %>%
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select(sort(names(.)))
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seq_df_sample <- lapply(seq_df, function(df) {
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df$Z2
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}) %>% reduce(left_join, by = "Rank1")
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seq_df_sample_lodes <- to_lodes_form(seq_df_sample, key = "x", axes = 2:5)
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seq_df_otu_lodes <- to_lodes_form(seq_df_otu, key = "x", axes = 6:9)
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```
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```{r}
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mach_metadata <- read.table(file = "data/mach/kinetic_sample_metadata.tsv") %>% rownames_to_column(var = "Rank1")
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seq_df_sample_lodes <- left_join(seq_df_sample_lodes, mach_metadata)
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ggplot(seq_df_sample_lodes, aes(x = x, alluvium = alluvium, stratum = stratum, label = stratum)) +
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geom_alluvium(aes(fill = Weaned)) +
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geom_stratum() +
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geom_text(stat = "stratum")
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ggplot(seq_df_otu_lodes, aes(x = x, alluvium = alluvium, stratum = stratum, label = stratum)) +
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geom_alluvium(aes(fill = Rank2)) +
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geom_stratum() +
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geom_text(stat = "stratum")
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``` |