---
title: "1. WikiPathways visualization"
author: "by Jarno Koetsier"
package: PinPath
date: "`r Sys.Date()`"
output: 
    BiocStyle::html_document:
    toc: true
    toc_depth: 2
    includes:
      in_header: Pathway-Visualization-schema.html
# pdf_document:
#   toc: true
vignette: >
    %\VignetteIndexEntry{1. WikiPathways visualization}
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}
---

```{r setup, echo=FALSE, results="hide"}
knitr::opts_chunk$set(
    tidy = FALSE,
    cache = FALSE,
    dev = "png",
    message = FALSE, error = FALSE, warning = TRUE)
```

# Introduction
PinPath allows you to visualize your data onto pathways diagrams, 
and pinpoint where the relevant changes occur. Results from (epi)genomics,
transcriptomics, (phospho)proteomics, metabolomics and many more experiments 
can be visualized onto pathway diagrams from **WikiPathways** and **KEGG**. 
You can also visualize your own custom GPML and KGML files. As long as 
your data can be linked to genes, proteins, or metabolites, you can visualize 
it using PinPath.

<br>
This vignette will cover visualizing differential expression analysis results 
onto **WikiPathways** pathway diagrams.

# Installation
First, make sure you install and load all necessary packages.
```{r install-pinpath, message = FALSE, warning = FALSE, eval=FALSE}
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")

BiocManager::install("PinPath")
```

Besides PinPath, we will also use the *rWikipathways* and *org.Hs.eg.db* 
packages in this vignette.
```{r install-others, message = FALSE, warning = FALSE, eval=FALSE}
library(PinPath)
library(rWikiPathways)
library(org.Hs.eg.db)
```

# Dataset
The example dataset we will use compares the expression of transcripts in 
lung cancer biopsies versus normal tissue. Differential expression analysis 
has already been performed, generating log2FCs and p-values for each gene. 
```{r dataset, message = FALSE, warning = FALSE}
lung_expr <- read.csv(
    system.file("extdata","data-lung-cancer.csv", package ="PinPath"), 
    stringsAsFactors = FALSE)
```

In the pathway, we want to show which gene is significantly differentially 
expressed. For this, we will use an adjusted p-value cutoff of 0.05.
```{r significance, results = 'asis'}
lung_expr$Significant <- ifelse(lung_expr$adj.P.Value < 0.05, "Yes", "No")
```

# Set colors
After we have loaded and prepared the differential expression analysis 
statistics, we need to define how to color the statistics in the pathway 
diagram. In this vignette, we will plot the log2FC and significance of each 
gene on the pathway diagram. We can start by loading the default color palette.
```{r default-color-values}
colorList <- PinPath::defaultColorList(lung_expr[,c("log2FC", "Significant")])
```

In the next step, we can adjust the default color palette to the desired color 
values. For instance, we want to display a green color when a gene is 
differentially expressed  and a white color when it is not.
```{r modify-significant-color}
colorList[["Significant"]]$Color <- c(
    "Yes" = "green",
    "No" = "white")
```

Furthermore, we can set the minimum and maximum value of the log2FC color
gradient to -1.5 and 1.5, respectively. Note that values exceeding these bounds 
are clipped and mapped to the colors representing the respective minimum or 
maximum.
```{r modify-log2FC-color}
colorList[["log2FC"]]$ColorVal <- c(
    "MinVal" = -1.5,
    "MidVal" = 0,
    "MaxVal" = 1.5)
```

# Plot pathway
We can now plot the differential expression statistics on the 
*WP5087: Pleural mesothelioma* pathway.
If not specified otherwise, the pathway and legend image will be saved in 
your working directory. The pathway image will be opened by default.
```{r plot-pathway, message = FALSE, warning = FALSE}
# WP5087: Pleural mesothelioma
pathway_id <- "WP5087"
infile <- rWikiPathways::getPathway(pathway_id)

# Draw pathway
pathVis <- PinPath::drawGPML(
    infile = infile,
    annGenes = "org.Hs.eg.db",
    inputDB = "ENSEMBL",
    featureIDs = lung_expr$GeneID,
    colorVar = lung_expr[,c("log2FC", "Significant")],
    colorList = colorList,
    nodeTable = TRUE,
    legend = TRUE,
    openFile = FALSE) # <-- set to TRUE to open the image automatically
```

Pathway image:
<img src="Pleural_mesothelioma_WP5087_r140461_Homo_sapiens.svg" 
width="1000">

Legend image:
<img src="legend_Pleural_mesothelioma_WP5087_r140461_Homo_sapiens.svg" 
width="500">

# Plot network
You can also plot the pathway as a network. In contrast to the pathway diagram, 
every element (e.g., gene/protein) is represented exactly once in the network.
```{r plot-network, message = FALSE, warning = FALSE}
pathVis <- PinPath::GPML2Network(
    infile = infile,
    annGenes = "org.Hs.eg.db",
    inputDB = "ENSEMBL",
    featureIDs = lung_expr$GeneID,
    colorVar = lung_expr[,c("log2FC", "Significant")],
    colorList = colorList,
    nodeSize = 0.5,
    nodeTable = TRUE,
    legend = FALSE,
    openFile = FALSE) # <-- set to TRUE to open the image automatically
```

Network image:
<img src="network_Pleural_mesothelioma_WP5087_r140461_Homo_sapiens.svg" 
width="1000">

Legend image:
<img src="legend_Pleural_mesothelioma_WP5087_r140461_Homo_sapiens.svg" 
width="500">

# Session info

```{r sessionInfo}
sessionInfo()
```