kernel_1.Rmd

---
title: "Kernels "
author: "UIB"
date: "`r Sys.Date()`"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE,cache=TRUE)
```

# Define experiment and load data

The results of MetaDag Web Tool areat the folder

```{r}
experiment="result_9ed945b7-6fd7-30de-80a3-01b4e8528ebf"
path=paste0("data/result_9ed945b7-6fd7-30de-80a3-01b4e8528ebf","/data/")
path
setwd("data/result_9ed945b7-6fd7-30de-80a3-01b4e8528ebf/data/Individuals/")
dir()
```

# Read all graphs from a level of the experiment

Read all graphs from a level from experiment; for example individuals. We read only firts (alphabetic)  two graph

```{r}
list_names=dir(paste0(path,"Individuals/"))
list_names
list_names= list_names[-1] # filter 0000_RefPw
length(list_names)
k=length(list_names)
list_names= list_names[1:k] # select ONLY 5 individuals
list_names
dir(paste0("Individuals/",list_names[1],"/"))
library(igraph)
graphs_list=paste0(path,"Individuals/",list_names,"/",list_names,"_MDAG.graphml")
g_MDAG_list=
  lapply(graphs_list,FUN=function(x) read.graph(file=x,
                    format="graphml"))
names(g_MDAG_list)=list_names
summary(g_MDAG_list[[1]])
head(as_long_data_frame(g_MDAG_list[[1]]))

```


**Graph Kernels package**

[graphkernels: R and Python packages for graph comparison](https://academic.oup.com/bioinformatics/article/34/3/530/4209994?login=true)
statGraph’
[Discriminating Different Classes of Biological Networks by Analyzing the Graphs Spectra Distribution](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0049949)

```{r}
plot.igraph(g_MDAG_list[[1]],layout=layout_as_tree,
            label=NA,label.cex=0)
```


```{r}
knitr::include_graphics("data/result_9ed945b7-6fd7-30de-80a3-01b4e8528ebf/data/Individuals/cang/cang_mDAG.svg")
```

```{r}
knitr::include_graphics("data/result_9ed945b7-6fd7-30de-80a3-01b4e8528ebf/data/Individuals/cang/cang_mDAG_essential.svg")
```

```{r}
knitr::include_graphics("data/result_9ed945b7-6fd7-30de-80a3-01b4e8528ebf/data/Individuals/cang/cang_RC.svg")
```


```
library(DOT)
dot("raw_data/result_d34a984d-d1ba-38d9-9c20-642ef834bbcd/data/Individuals/aag/aag_mDAG2.dot",return="svg")
```