<!--- 
This report create a scatterplot of a dataset and variables of interest.

Input parameters:
 
* Report-specific
- reportTitle: string with report title
- reportTitleLevel: integer with level of the report title, 1 for chapter, 2 for section, ...
- dataFileName: string with name of the file of interest
- dataProcessing (optional): list with parameters for data processing, see ? clinDataReview::processData
- loopingVar (optional): character vector with variables to loop over, a plot will be created for each combination of groups of this variable
- loopingNMax (optional): integer with maximal number of groups to consider (all by default)
- plotFunction: string with name of a plotting function of interest, available in the clinDataReview package
- plotParams: list with plotting parameters passed to the 'plotFunction' function
(excepted: 'data', 'labelVars', 'table', 'pathVar', 'id' and 'verbose')

* General:
- pathDataFolder: string with path to the data folder
- patientProfilePath: string with relative path where patient profiles are stored

-->

```{r plotTemplate-options, echo = FALSE, warning = FALSE, message = FALSE}

library(knitr)
knitr::opts_chunk$set(
	echo = FALSE, 
	warning = FALSE, error = FALSE, message = FALSE, 
	results = "asis"
)

knitr::knit_hooks$set(
	message = function(x, options) {
		paste('\n\n<div class="alert alert-info">',
			gsub('##', '\n', x),
			'</div>', sep = '\n')
	}
)

# print warnings where they occur (warn = 0 by default)
options(warn = 1)

```

```{r plotTemplate-attachParameters}

# Note: find a way to specify defaults for variables
attach(params)
if(!exists("loopingVar")) loopingVar <- NULL
if(!exists("comparisonTableType"))	comparisonTableType <- "none"
if(comparisonTableType != "none" & 
		(!exists("pathDataFolderOld") || !file.exists(file.path(pathDataFolderOld, dataFileName)))
		){
	warning("No comparison table is included because data from previous batch is not available.")
	comparisonTableType <- "none"
}
if(!comparisonTableType %in% c("none", "newData-diff")){
	warning("Option:", comparisonTableType, "is not available for the plot template",
		"no comparison is included.")
	comparisonTableType <- "none"
}
if(!exists("patientProfilePath"))	patientProfilePath <- NULL

```

```{r plotTemplate-loadPackages}

library(clinDataReview)
library(clinUtils)
library(plyr) # for dlply, rbind.fill

if(exists("tableParams"))
	library(inTextSummaryTable)

```

```{r plotTemplate-startUpCode, code = as.character(params$startup)}
```

```{r plotTemplate-setTitle}

if(!exists("reportTitleLevel"))	reportTitleLevel <- 1

# Create a header at the wanted depth
cat(getMdHeader(title = reportTitle, level = reportTitleLevel))

```


```{r plotTemplate-getData}

# Load data
if(comparisonTableType != "none") {
	
	pathsData <- c(
		"currentData" = pathDataFolder,
		"previousData" = pathDataFolderOld
	)	
	
} else pathsData <- c("currentData" = pathDataFolder)

dataList <- sapply(names(pathsData), function(dataBatch) {

	pathDataBatch <- pathsData[[dataBatch]]
			
	pathData <- file.path(pathDataBatch, dataFileName)
	dataAll <- loadDataADaMSDTM(pathData, verbose = FALSE)
	data <- do.call(plyr::rbind.fill, dataAll)
	
	# Extract label information
	labelVars <- attr(dataAll, "labelVars")
	
	# Data processing 
	if(exists("dataProcessing")){
		data <- processData(
			data = data, 
			dataPath = pathDataBatch,
			processing = dataProcessing,
			verbose = TRUE,
			labelVars = labelVars
		)
		# Labels updated with extra annotation:
		labelVars <- attr(data, "labelVars")
	}
	
	# Create URL to patient profiles
	if(!is.null(patientProfilePath))
		data <- createPatientProfileVar(
			data = data, 
			patientProfilePath = patientProfilePath,
			checkExist = FALSE
		)
	
	data
	
}, simplify = FALSE)

data <- dataList$currentData
labelVars <- attr(dataList$currentData, "labelVars")

```

```{r plotTemplate-computeSummaryStatisticsTable, eval = exists("tableParams") & nrow(data) > 0}
  
dataList <- sapply(dataList, function(dataBatch) {

	# Compute summary statistics
	tableParamsBatch <- params[["tableParams"]]
	tableParamsBatch$data <- dataBatch
	summaryTable <- do.call(computeSummaryStatisticsTable, tableParamsBatch)	
	summaryTable <- subset(summaryTable, !isTotal)
	
	# extra processing if required
	if(exists("tableProcessing")){
		
		summaryTable <- processData(
			data = summaryTable, 
			processing = tableProcessing,
			verbose = FALSE,
			labelVars = labelVars,
			labelData = "summary table"
		)
		labelVars <- attr(summaryTable, "labelVars")
		
	}
	
	# add summary statistics to input data
	dataBatchWithStats <- base::merge(
		x = dataBatch, y = summaryTable, 
		all.x = TRUE, sort = FALSE
	)
	attr(dataBatchWithStats, "labelVars") <- labelVars
	dataBatchWithStats
	
}, simplify = FALSE)

data <- dataList$currentData
labelVars <- attr(dataList$currentData, "labelVars")

```

```{r plotTemplate-createTable, eval = (comparisonTableType == "newData-diff")}

dataPrevious <- dataList$previousData
dataCurrent <- dataList$currentData
if(!exists("comparisonTableParams"))	comparisonTableParams <- NULL

# By default, reference variables are the variables displayed by default 
# in the table attached to the plot
if(is.null(comparisonTableParams$referenceVars)){
	
	argsPlot <- plotParams
	argsPlot$labelVars <- labelVars
	referenceVars <- getPlotTableVars(plotFunction, plotArgs = argsPlot)
	
	# add looping var (in case e.g. replicated records across looping vars)
	referenceVars <- c(referenceVars, loopingVar)
	
	referenceVars <- setdiff(referenceVars, "Comparison type")
	
	comparisonTableParams$referenceVars <- referenceVars
	comparisonTableParams$changeableVars <- NULL
	
}

argsCompTable <- c(
	list(
		newData = dataCurrent,
		oldData = dataPrevious,
		outputType = comparisonTableType
	),
	comparisonTableParams
)
outputComparison <- do.call(clinUtils::compareTables, argsCompTable)

if(!is.null(outputComparison)){
	
	data <- outputComparison
	
	tableVars <- plotParams$tableVars
	if(is.null(tableVars)){
		tableVars <- c(argsCompTable$referenceVars, argsCompTable$changeableVars)
		tableVars <- setdiff(tableVars, loopingVar)
	}

	tableVars <- c("Comparison type", tableVars)
	plotParams$tableVars <- tableVars
	
}

```

```{r plotTemplate-createPlot}

if(!is.null(loopingVar)){
	
	# format label for 'knitPrintClinDataReview'
	data[, loopingVar] <- colwise(function(x) gsub("\\.", "", x))(data[, loopingVar, drop = FALSE])
	
	# only subset of the data if requested in _bookdown.yml
	if(exists("loopingNMax") &&	is.integer(loopingNMax)){
		
		data <- merge(
			x = data,
			y = unique(data[, loopingVar, drop = FALSE])[seq_len(loopingNMax), , drop = FALSE],
			all = FALSE
		)
		
	}
	
}
listPlots <- dlply(data, loopingVar, function(dataI){
			
	# Create plot unique ID
	argsLabel <- c(
		list("plotTemplate"),
		if(!is.null(loopingVar))	unique(dataI[, loopingVar, drop = FALSE])
	)		
	id <- do.call(formatLabel, argsLabel)
	
	# Create the plot
	argsPlot <- forceParams(plotParams)
	argsPlot$data <- dataI
	argsPlot$labelVars <- labelVars
	argsPlot$table <- TRUE
	argsPlot$pathVar = if(!is.null(patientProfilePath))	"patientProfilePath"
	argsPlot$id <- id
	
	do.call(plotFunction, argsPlot)	
	
})

knitPrintClinDataReview(
	list = listPlots,
	level = reportTitleLevel + 1
)

```
