load_data.qmd

# Load data

```{r setup_load_data, include=FALSE,message=FALSE}
knitr::opts_chunk$set(echo = TRUE,
                      cache=TRUE,
                      warning = FALSE,
                      message = FALSE, 
                      out.width = "100%",
                      lazy.cache = FALSE)
#pdf="TRUE"
library(tidyverse)
library(igraph)
library(ComplexHeatmap)
library(viridis)
library(circlize)
library(plotly)
library(randomcoloR)
library(factoextra)
library(RColorBrewer)
library(kableExtra)
library(igraph)
library(GGally)
```

```{r}
experiment=
  "0a845f74-826e-3b46-aed9-e7ecf74db262/"
path_exp=paste0("data/",experiment)
knitr::kable(data.frame(
  Directory_files_and_folders=dir(path_exp),
  Type=c(rep("Data file",2),
         rep("Directory",3),
         rep("Data file",8),
         "Directory")))
```

```{r}
MBB=read_csv(paste0(path_exp,"Different_MBB.csv"),
             show_col_types = FALSE)
mDAG=read_csv(paste0(path_exp,"Different_mDAG.csv"),
              show_col_types = FALSE)
```

## Load metadata

Organisms are sorted by Kingdom, Phylum and Class:

```{r}
path_exp
Results=read_csv(paste0(path_exp,"Results.csv"))
#rename MetaDaG variables
names(Results)[c(1,2,3,4,5)]=c("Organism","Categories","Groups","mDAG_Id","Full_Name")
taxo=Results %>% select(Organism:Full_Name)
meta_taxo=taxo %>% separate(Categories,into=c("Kingdom","Phylum","Class"))
index=which(is.na(meta_taxo$Class))
meta_taxo$Class[index]=paste(meta_taxo$Phylum[index])
rm(taxo)
aux=table(meta_taxo$Kingdom)
Freq_Kingdom=tibble(Kingdom=names(aux),Freq_Kingdom=aux)
aux=table(meta_taxo$Phylum)
Freq_Phylum=tibble(Phylum=names(aux),Freq_Phylum=aux)
aux=table(meta_taxo$Class)
Freq_Class=tibble(Class=names(aux),Freq_Class=aux)

meta_taxo = meta_taxo %>%
    left_join(Freq_Kingdom) %>% 
  left_join(Freq_Phylum) %>%
  left_join(Freq_Class)
meta_taxo = meta_taxo %>% 
  arrange(desc(Freq_Kingdom),
          desc(Freq_Phylum),
          desc(Freq_Class))

#arrange metaxto by frequencies of kingom phylum and class


knitr::kable(head(meta_taxo))
```

```{r}
table(meta_taxo$Kingdom) %>% kable %>%
  kable_styling("striped", full_width = F,position="left")%>% 
  scroll_box(width = "400px", height = "200px")
table(meta_taxo$Phylum,meta_taxo$Kingdom) %>% kable %>%
  kable_styling("striped", full_width = F,position="left")%>% 
  scroll_box(width = "500px", height = "500px")
```

## Table of MBBs

In this example `MBB` is a table with `r nrow(MBB)` rows and `r ncol(MBB)` columns. It displays, for every MBB, the selected groups (Kingdoms, families, etc.) to which it belongs.

```{r}
#100
knitr::kable(MBB[1:20,1:10]) %>%   
  scroll_box(width = "100%", height = "200px")
```

## Table of m-DAGs

In this example `mDAG` is a table with `r nrow(mDAG)` rows and `r ncol(mDAG)` columns. It displays, for every m-DAG, the selected groups (Kingdoms, families, etc.) in which it belongs.

```{r}
kable(mDAG[1:20,1:10]) %>%   scroll_box(width = "100%", height = "200px")
```

```{r}
dim(mDAG)
names(mDAG)[1:6]
head(names(mDAG)[7:(dim(mDAG)[2]-1150)])
# 28 to 1213  code MBB: 1 if MBB in mDAG 0
```

## Results Table

The `Results` table contains for every organism (row) the following information: its category (taxonomy), selected group, Full name, m-DAG id and all reactions name id with their corresponding enzyme. When a reaction is present in the corresponding m-DAG, the MBB to which it belongs is displayed in this column.

```{r}
kable(Results[1:20,1:10])%>%
  row_spec(0, angle = 0) %>%   
  scroll_box(width = "300%", height = "1000px")
```

```{r}
dim(Results)
names(Results)[1]# organisms  kegg id  class representant of mDAG
names(Results)[2]# taxonomy separate by |
names(Results)[3]# groups 
names(Results)[4]# mDAG_Id 
names(Results)[5]# Full name representant
names(Results)[6:36]# columns 6 to 3998 
# reactions name id with its enzyme.
```

```{r}
reactions=names(Results)[-c(1:5)]
reverse_reactions=stringr::str_detect(reactions,"rev")
reverse_reactions=table(reverse_reactions)
dimnames(reverse_reactions)$reverse_reactions=
  c("Non reverse reaction","Reverse reaction")
reverse_reactions %>% kable %>%
  kable_styling("striped", full_width = F,position="left")
```

```{r pasar_load, include=FALSE}
save.image(file='metadag_work_space.RData')
```