# Analisis de funcionalidad

```{r}

#paquetes a utilizar

library(microeco)

library(file2meco)

library(agricolae)

library(phyloseq)

library(microbiome)

```

## Semana 0

```{r}

# convertir de un objeto phyloseq a uno de microtable

meco_dataset <- phyloseq2meco(p_0week)

meco_dataset

# Functional enrichment

t1 <- trans_func$new(meco_dataset)

t1$cal_spe_func(prok_database = "FAPROTAX")

t1$cal_spe_func_perc(abundance_weighted = TRUE)

# use list to prepare data

tmp <- list()

# transpose res_spe_func_perc to be a data.frame like taxonomic abundance

tmp$func <- as.data.frame(t(t1$res_spe_func_perc), check.names = FALSE)

# assign the list as taxa_abund in your microtable object

meco_dataset$taxa_abund <- tmp

# use trans_diff class to perform differential test

# Acá debes usar una comparación adecuada, por ejemplo: estado de salud, es decir una columna

# de tu sample_data(GlobalPatterns), en este caso usé SampleType

t2 <- trans_diff$new(dataset = meco_dataset, method = "anova", group = "groups", taxa_level = "all")

t2$plot_diff_abund(add_sig = T, color_values =c("#EE7600", "#008B8B")) + ggplot2::ylab("Relative abundance (%)")

ggsave("~/tesis/03_Output/funcion.png", dpi=600,width = 21,

height = 13)

```

## pacientes con MDD semana 0 y 8

```{r}

# convertir de un objeto phyloseq a uno de microtable

meco_dataset <- phyloseq2meco(p_mdd)

meco_dataset

# Functional enrichment

t1 <- trans_func$new(meco_dataset)

t1$cal_spe_func(prok_database = "FAPROTAX")

t1$cal_spe_func_perc(abundance_weighted = TRUE)

# use list to prepare data

tmp <- list()

# transpose res_spe_func_perc to be a data.frame like taxonomic abundance

tmp$func <- as.data.frame(t(t1$res_spe_func_perc), check.names = FALSE)

# assign the list as taxa_abund in your microtable object

meco_dataset$taxa_abund <- tmp

# use trans_diff class to perform differential test

t2 <- trans_diff$new(dataset = meco_dataset, method = "anova", group = "weeks", taxa_level = "all")

t2$plot_diff_abund(add_sig = T, color_values =c("#00868B", "#8B3A62")) + ggplot2::ylab("Relative abundance (%)")

ggsave("~/tesis/03_Output/funcion_dd.png", dpi=600,width = 21,

height = 13)

```