---
title: 'MetaGxOvarian: A Package for Ovarian Cancer Gene Expression Analysis'

author:
- name: Michael Zon
  affiliation:
    - &pm Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- name: Deena M.A. Gendoo
  affiliation:
    - *pm
    - &mbp Department of Medical Biophysics, University of Toronto, Toronto, Canada
- name: Natchar Ratanasirigulchai
  affiliation:
    - *pm
- name: Gregory Chen
  affiliation:
    - *mbp
- name: Levi Waldron
  affiliation:
    - &dfc Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
    - &hpc Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
- name: Benjamin Haibe-Kains
  email: benjamin.haibe.kains@utoronto.ca
  affiliation:
    - *mbp

output: BiocStyle::pdf_document

vignette: >
  %\VignetteEngine{knitr::knitr}
  %\VignetteIndexEntry{MetaGxOvarian: A Package for Ovarian Cancer Gene Expression Analysis}
---

```{r knitr_opts, include=FALSE, message=FALSE, warning=FALSE}
library(xtable)
```

# Installing the Package

The MetaGxOvarian package is a compendium of Ovarian Cancer datasets.
The package is publicly available and can be installed from Bioconductor into R version 3.6.0 or higher.

To install the MetaGxOvarian package from Bioconductor:
```{r install-pkg, eval=FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("MetaGxOvarian")
```

# Loading Datasets

First we load the MetaGxOvarian package into the workspace.

To load the packages into R, please use the following commands:

```{r loadlib, message=FALSE, warning=FALSE}
library(MetaGxOvarian)
esets <- MetaGxOvarian::loadOvarianEsets()[[1]]
```

This will load 26 expression datasets. Users can modify the parameters of the 
function to restrict datasets that do not meet certain criteria for loading. 
Some example parameters are shown below:

- `keepCommonOnly`: Retain only genes that are common across all platforms loaded (default = FALSE)
- `minSampleSize`: Retain studies with a minimum sample size (default = 0)
- `minNumberGenes`: Retain studies with a minimum number of genes (default = 0)
- `minNUmberEvents`: Retain studies with a minimum number of survival events (default = 0)
- `removeDuplicates`: Remove duplicate samples (default = TRUE)

# Obtaining Sample Counts in Datasets

```{r sample_number_summary}
numSamples <- vapply(seq_along(esets), FUN=function(i, esets) {
    length(sampleNames(esets[[i]]))
    }, numeric(1), esets=esets)


SampleNumberSummaryAll <- data.frame(NumberOfSamples = numSamples,
                                     row.names = names(esets))
total <- sum(SampleNumberSummaryAll[,"NumberOfSamples"])
SampleNumberSummaryAll <- rbind(SampleNumberSummaryAll, total)
rownames(SampleNumberSummaryAll)[nrow(SampleNumberSummaryAll)] <- "Total"

xtable(SampleNumberSummaryAll, digits = 2)
```

# Access Phenotype Data

We can also obtain a summary of the phenotype data (pData) for each expression dataset.
Here, we assess the proportion of samples in every datasets that contain a specific pData variable.

```{r sample_number_summaries_pdata}
pDataID <- c("sample_type", "histological_type", "primarysite", "summarygrade",
             "summarystage", "tumorstage", "grade",
             "age_at_initial_pathologic_diagnosis", "pltx", "tax",
             "neo", "days_to_tumor_recurrence", "recurrence_status",
             "days_to_death", "vital_status")


pDataPercentSummaryTable <- NULL
pDataSummaryNumbersTable <- NULL

pDataSummaryNumbersList = lapply(esets, function(x)
  vapply(pDataID, function(y) sum(!is.na(pData(x)[,y])), numeric(1)))

pDataPercentSummaryList = lapply(esets, function(x)
  vapply(pDataID, function(y)
    sum(!is.na(pData(x)[,y]))/nrow(pData(x)), numeric(1))*100)

pDataSummaryNumbersTable = sapply(pDataSummaryNumbersList, function(x) x)
pDataPercentSummaryTable = sapply(pDataPercentSummaryList, function(x) x)

rownames(pDataSummaryNumbersTable) <- pDataID
rownames(pDataPercentSummaryTable) <- pDataID
colnames(pDataSummaryNumbersTable) <- names(esets)
colnames(pDataPercentSummaryTable) <- names(esets)

pDataSummaryNumbersTable <- rbind(pDataSummaryNumbersTable, total)
rownames(pDataSummaryNumbersTable)[nrow(pDataSummaryNumbersTable)] <- "Total"


# Generate a heatmap representation of the pData
pDataPercentSummaryTable<-t(pDataPercentSummaryTable)
pDataPercentSummaryTable<-cbind(Name=(rownames(pDataPercentSummaryTable))
                                ,pDataPercentSummaryTable)

nba<-pDataPercentSummaryTable
gradient_colors = c("#ffffff","#ffffd9","#edf8b1","#c7e9b4","#7fcdbb",
                    "#41b6c4","#1d91c0","#225ea8","#253494","#081d58")

library(lattice)
nbamat<-as.matrix(nba)
rownames(nbamat)<-nbamat[,1]
nbamat<-nbamat[,-1]
Interval<-as.numeric(c(10,20,30,40,50,60,70,80,90,100))

levelplot(nbamat,col.regions=gradient_colors,
          main="Available Clinical Annotation",
          scales=list(x=list(rot=90, cex=0.5),
                      y= list(cex=0.5),key=list(cex=0.2)),
          at=seq(from=0,to=100,length=10),
          cex=0.2, ylab="", xlab="", lattice.options=list(),
          colorkey=list(at=as.numeric(factor(c(seq(from=0, to=100, by=10)))),
                  labels=as.character(c( "0","10%","20%","30%", "40%","50%",
                                         "60%", "70%", "80%","90%", "100%"),
                                      cex=0.2,font=1,col="brown",height=1,
                                      width=1.4), col=(gradient_colors)))
```

# Session Info
```{r sessinInfo, echo=FALSE, eval=TRUE}
sessionInfo()
```