polarolouis/human-microbiome-compendium
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Modif analysis

Browse source
This commit is contained in:
Louis 2026-02-02 16:34:05 +01:00
parent 1fc536e0f0
commit 819d4328c0
2 changed files with 3944 additions and 5 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

3938
analysis_benchmark_lbm_seq.html Normal file
View file

File diff suppressed because one or more lines are too long

11
analysis_benchmark_lbm_seq.qmd
View file

@ -11,7 +11,7 @@ library(tidyverse)
library(phyloseq) library(phyloseq)
library(biomformat) library(biomformat)
source("utils.R") source("utils.R")
mach_data <- import_biom("data/mach/kinetic.biom")
the_data <- import_biom("data/chaillou/chaillou.biom") the_data <- import_biom("data/chaillou/chaillou.biom")
per_taxa_networks <- collapse_otu_at_taxo(the_data) per_taxa_networks <- collapse_otu_at_taxo(the_data)
otu_df <- sapply(per_taxa_networks, nrow) %>% otu_df <- sapply(per_taxa_networks, nrow) %>%
@ -20,7 +20,7 @@ otu_df <- sapply(per_taxa_networks, nrow) %>%
rename(Nb_OTU = ".", Rank = "rowname") rename(Nb_OTU = ".", Rank = "rowname")
flist <- list.files(here("results", "lbm-seq"), full.names = TRUE, pattern = ".Rds") flist <- list.files(here("results", "lbm-seq", "chaillou"), full.names = TRUE, pattern = ".Rds")
para_flist <- grepv(pattern = "para.Rds", flist) para_flist <- grepv(pattern = "para.Rds", flist)
seq_flist <- grepv(pattern = "seq.Rds", flist) seq_flist <- grepv(pattern = "seq.Rds", flist)
@ -107,7 +107,7 @@ Tous les Z sont concordants entre les répétitions, je vais donc sélectionner
Ci-après on extrait les premiers modèles. Ci-après on extrait les premiers modèles.
```{r} ```{r}
seq_model <- purrr::transpose(seq_results)[[2]] seq_model <- purrr::transpose(seq_results)[[1]]
para_model <- purrr::transpose(para_results)[[1]] para_model <- purrr::transpose(para_results)[[1]]
notrans_model <- purrr::transpose(notrans_results)[[1]] notrans_model <- purrr::transpose(notrans_results)[[1]]
``` ```
@ -178,11 +178,12 @@ seq_df_otu_lodes <- to_lodes_form(seq_df_otu, key = "x", axes = 6:9)
```{r} ```{r}
mach_metadata <- read.table(file = "data/mach/kinetic_sample_metadata.tsv") %>% rownames_to_column(var = "Rank1") mach_metadata <- read.table(file = "data/mach/kinetic_sample_metadata.tsv") %>% rownames_to_column(var = "Rank1")
chaillou_metadata <- read.table(file = "data/chaillou/sample_metadata.tsv") %>% rownames_to_column(var = "Rank1")
seq_df_sample_lodes <- left_join(seq_df_sample_lodes, mach_metadata) seq_df_sample_lodes <- left_join(seq_df_sample_lodes, chaillou_metadata)
ggplot(seq_df_sample_lodes, aes(x = x, alluvium = alluvium, stratum = stratum, label = stratum)) + ggplot(seq_df_sample_lodes, aes(x = x, alluvium = alluvium, stratum = stratum, label = stratum)) +
geom_alluvium(aes(fill = Weaned)) + geom_alluvium(aes(fill = EnvType)) +
geom_stratum() + geom_stratum() +
geom_text(stat = "stratum") geom_text(stat = "stratum")