07-summary.Rmd

---
author: V. Keith Hughitt
date: "`r format(Sys.time(), '%d %B, %Y')`"
title: "Host-parasite consensus network analysis results"
params:
  version: ""
output:
  html_document:
    theme: cosmo
    toc: true
    toc_float: true
    number_sections: true
    code_folding: hide
  pdf_document:
    toc: true
    latex_engine: xelatex
---

Overview
========

```{r load_libraries, message=FALSE}
library(dplyr)
library(igraph)
library(knitr)
library(readr)
library(rJava)
library(printr)

output_tabledir <- 'output/1.0/07-summary/table'

if (!dir.exists(output_tabledir)) {
    dir.create(output_tabledir, recursive=TRUE)
}

options(stringsAsFactors=FALSE)

set.seed(1)

# knitr options
opts_chunk$set(dev=c('png', 'pdf'),
               fig.width=6,
               fig.height=6,
               fig.retina=1,
               dpi=600)
```

```{r setup}
datasets <- data.frame(
    short=c('HsLm-inf', 'HsLm-uninf', 'HsTc-inf', 'HsTc-uninf', 'Lmajor', 'Tcruzi'),
    long =c('Human infected with L. major', 'Human infected with L. major (uninfected samples)',
            'Human infected with T. cruzi', 'Human infected with T. cruzi (uninfected samples)',
            'L. major (all samples)', 'T. cruzi (all samples)')
)
```


Results
=======

### Consensus network vs. Individual networks

```{r consensus_network_vs_indiv_nets, results='asis', message=FALSE}
# load tables for each dataset
#for (x in Sys.glob('output/1.0/01-network-comparison/table/table_01_*')) {
table_01 <- data.frame(type=c("GO Terms", "KEGG Pathways", "CPDB Pathways", "Marbach TF Genes"))

for (ds in datasets$short) {
    infile <- sprintf("output/1.0/01-network-comparison/table/table_01_%s.csv", tolower(ds))

    # skip if file doesn't exist
    if (!file.exists(infile)) {
        next
    }

    #long <- datasets$long[match(ds, datasets$short)]
    dat <- read_csv(infile) %>%
        select(-score)
    colnames(dat) <- c('type', ds)

    table_01 <- merge(table_01, dat, by='type', all=TRUE)
}

kable(table_01, digits=2)
```

```{r child='child/00-save-tables.Rmd'}
```